Package: a4 Version: 1.46.0 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats License: GPL-3 MD5sum: 4fe2823df78513c79777d009196856fd NeedsCompilation: no Package: a4Base Version: 1.46.0 Depends: a4Preproc, a4Core Imports: methods, graphics, grid, Biobase, annaffy, mpm, genefilter, limma, multtest, glmnet, gplots Suggests: Cairo, ALL, hgu95av2.db, nlcv Enhances: gridSVG, JavaGD License: GPL-3 MD5sum: 86bfcbf8ca4d02774d1057a304193571 NeedsCompilation: no Package: a4Classif Version: 1.46.0 Depends: a4Core, a4Preproc Imports: methods, Biobase, ROCR, pamr, glmnet, varSelRF, utils, graphics, stats Suggests: ALL, hgu95av2.db, knitr, rmarkdown License: GPL-3 MD5sum: 4caa10169797e6ee42ca1a05671274a6 NeedsCompilation: no Package: a4Core Version: 1.46.0 Imports: Biobase, glmnet, methods, stats Suggests: knitr, rmarkdown License: GPL-3 MD5sum: aee4c7414982df8ade728081971c0923 NeedsCompilation: no Package: a4Preproc Version: 1.46.0 Imports: BiocGenerics, Biobase Suggests: ALL, hgu95av2.db, knitr, rmarkdown License: GPL-3 MD5sum: 31a1f22866a1faad83cbf64561520b11 NeedsCompilation: no Package: a4Reporting Version: 1.46.0 Imports: methods, xtable Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 386cb5d0edb3fa983f262a9043ad760f NeedsCompilation: no Package: ABarray Version: 1.66.0 Imports: Biobase, graphics, grDevices, methods, multtest, stats, tcltk, utils Suggests: limma, LPE License: GPL MD5sum: f841c4c885c64e9776bf0a6ea15cbb2a NeedsCompilation: no Package: abseqR Version: 1.16.0 Depends: R (>= 3.5.0) Imports: ggplot2, RColorBrewer, circlize, reshape2, VennDiagram, plyr, flexdashboard, BiocParallel (>= 1.1.25), png, grid, gridExtra, rmarkdown, knitr, vegan, ggcorrplot, ggdendro, plotly, BiocStyle, stringr, utils, methods, grDevices, stats, tools, graphics Suggests: testthat License: GPL-3 | file LICENSE MD5sum: d464cec5cfa502841cf5080b3018e048 NeedsCompilation: no Package: ABSSeq Version: 1.52.0 Depends: R (>= 2.10), methods Imports: locfit, limma Suggests: edgeR License: GPL (>= 3) MD5sum: aa240fabff9f675d35cc00883db80e12 NeedsCompilation: no Package: acde Version: 1.28.0 Depends: R(>= 3.3), boot(>= 1.3) Imports: stats, graphics Suggests: BiocGenerics, RUnit License: GPL-3 MD5sum: e56cb58b44f42acc784e183126551c5c NeedsCompilation: no Package: ACE Version: 1.16.0 Depends: R (>= 3.4) Imports: Biobase, QDNAseq, ggplot2, grid, stats, utils, methods, grDevices, GenomicRanges Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: c44aad495e4ae569b085f511a104b27b NeedsCompilation: no Package: aCGH Version: 1.76.0 Depends: R (>= 2.10), cluster, survival, multtest Imports: Biobase, grDevices, graphics, methods, stats, splines, utils License: GPL-2 MD5sum: 4ed40e84cdfa7084127e10a09349ee6e NeedsCompilation: yes Package: ACME Version: 2.54.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics Imports: graphics, stats License: GPL (>= 2) MD5sum: 349b793b503b19cfbfea1d60def06700 NeedsCompilation: yes Package: ADaCGH2 Version: 2.38.0 Depends: R (>= 3.2.0), parallel, ff, GLAD Imports: bit, DNAcopy, tilingArray, waveslim, cluster, aCGH, snapCGH Suggests: CGHregions, Cairo, limma Enhances: Rmpi License: GPL (>= 3) MD5sum: 48c49370d2dd3edb67ed26f7a4f8a5dd NeedsCompilation: yes Package: ADAM Version: 1.14.0 Depends: R(>= 3.5), stats, utils, methods Imports: Rcpp (>= 0.12.18), GO.db (>= 3.6.0), KEGGREST (>= 1.20.2), knitr, pbapply (>= 1.3-4), dplyr (>= 0.7.6), DT (>= 0.4), stringr (>= 1.3.1), SummarizedExperiment (>= 1.10.1) LinkingTo: Rcpp Suggests: testthat, rmarkdown License: GPL (>= 2) MD5sum: d6aad59a5d8720a7190d99bdb0a7ee44 NeedsCompilation: yes Package: ADAMgui Version: 1.14.0 Depends: R(>= 3.6), stats, utils, methods, ADAM Imports: GO.db (>= 3.5.0), dplyr (>= 0.7.6), shiny (>= 1.1.0), stringr (>= 1.3.1), stringi (>= 1.2.4), varhandle (>= 2.0.3), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), ggpubr (>= 0.1.8), ggsignif (>= 0.4.0), reshape2 (>= 1.4.3), RColorBrewer (>= 1.1-2), colorRamps (>= 2.3), DT (>= 0.4), data.table (>= 1.11.4), gridExtra (>= 2.3), shinyjs (>= 1.0), knitr, testthat Suggests: markdown, BiocStyle License: GPL (>= 2) MD5sum: 48cab0de50076fca376c39fe72c7ff4e NeedsCompilation: no Package: adductomicsR Version: 1.14.0 Depends: R (>= 3.6), adductData, ExperimentHub, AnnotationHub Imports: parallel (>= 3.3.2), data.table (>= 1.10.4), OrgMassSpecR (>= 0.4.6), foreach (>= 1.4.3), mzR (>= 2.14.0), ade4 (>= 1.7.6), rvest (>= 0.3.2), pastecs (>= 1.3.18), reshape2 (>= 1.4.2), pracma (>= 2.0.4), DT (>= 0.2), fpc (>= 2.1.10), doSNOW (>= 1.0.14), fastcluster (>= 1.1.22), RcppEigen (>= 0.3.3.3.0), bootstrap (>= 2017.2), smoother (>= 1.1), dplyr (>= 0.7.5), zoo (>= 1.8), stats (>= 3.5.0), utils (>= 3.5.0), graphics (>= 3.5.0), grDevices (>= 3.5.0), methods (>= 3.5.0), datasets (>= 3.5.0) Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5), Rdisop (>= 1.34.0), testthat License: Artistic-2.0 MD5sum: 5321e7ca95c807f02221ea10b1958767 NeedsCompilation: no Package: ADImpute Version: 1.8.0 Depends: R (>= 4.0) Imports: checkmate, BiocParallel, data.table, DrImpute, kernlab, MASS, Matrix, methods, rsvd, S4Vectors, SAVER, SingleCellExperiment, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 + file LICENSE MD5sum: 419c835ce2fc0487c405f8969c72493b NeedsCompilation: no Package: adSplit Version: 1.68.0 Depends: R (>= 2.1.0), methods (>= 2.1.0) Imports: AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db (>= 1.8.1), graphics, grDevices, KEGGREST (>= 1.30.1), multtest (>= 1.6.0), stats (>= 2.1.0) Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) License: GPL (>= 2) MD5sum: b43ed90820ddc28dbc1d10873d3040ba NeedsCompilation: yes Package: AffiXcan Version: 1.16.0 Depends: R (>= 3.6), SummarizedExperiment Imports: MultiAssayExperiment, BiocParallel, crayon Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: d65b4c5c4c8af5cb1e07cad498996bb5 NeedsCompilation: no Package: affxparser Version: 1.70.0 Depends: R (>= 2.14.0) Suggests: R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles License: LGPL (>= 2) MD5sum: 9898bbc5e7122f87d009435c84c4ba74 NeedsCompilation: yes Package: affy Version: 1.76.0 Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5) Imports: affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc LinkingTo: preprocessCore Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools License: LGPL (>= 2.0) MD5sum: 53cbffc6730bbac4cd93bbd70fb87414 NeedsCompilation: yes Package: affycomp Version: 1.74.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3) Suggests: splines, affycompData License: GPL (>= 2) MD5sum: 6d69d91c904478573b35eaeb6b536db7 NeedsCompilation: no Package: AffyCompatible Version: 1.58.0 Depends: R (>= 2.7.0), XML (>= 2.8-1), RCurl (>= 0.8-1), methods Imports: Biostrings License: Artistic-2.0 MD5sum: ba2f2f8dd8d5a678dc41d5fa86b322f8 NeedsCompilation: no Package: affyContam Version: 1.56.0 Depends: R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata Suggests: hgu95av2cdf License: Artistic-2.0 MD5sum: 6ac646aaf6051f868159a44820bdb5a9 NeedsCompilation: no Package: affycoretools Version: 1.70.0 Depends: Biobase, methods Imports: affy, limma, GOstats, gcrma, splines, xtable, AnnotationDbi, ggplot2, gplots, oligoClasses, ReportingTools, hwriter, lattice, S4Vectors, edgeR, RSQLite, BiocGenerics, DBI, Glimma Suggests: affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown License: Artistic-2.0 MD5sum: 1e54847013ece74e0191aecd71e3a85e NeedsCompilation: no Package: affyILM Version: 1.50.0 Depends: R (>= 2.10.0), methods, gcrma Imports: affxparser (>= 1.16.0), affy, graphics, Biobase Suggests: AffymetrixDataTestFiles, hgfocusprobe License: GPL-3 MD5sum: 1509b9ef9078f852665a022115b91018 NeedsCompilation: no Package: affyio Version: 1.68.0 Depends: R (>= 2.6.0) Imports: zlibbioc, methods License: LGPL (>= 2) MD5sum: 822b846100c156382ac0ae7ebd594878 NeedsCompilation: yes Package: affylmGUI Version: 1.72.0 Imports: grDevices, graphics, stats, utils, tcltk, tkrplot, limma, affy, affyio, affyPLM, gcrma, BiocGenerics, AnnotationDbi, BiocManager, R2HTML, xtable License: GPL (>= 2) MD5sum: ecca89124f55e0c161945ad32032df73 NeedsCompilation: no Package: affyPLM Version: 1.74.2 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), affy (>= 1.11.0), Biobase (>= 2.17.8), gcrma, stats, preprocessCore (>= 1.5.1) Imports: zlibbioc, graphics, grDevices, methods LinkingTo: preprocessCore Suggests: affydata, MASS License: GPL (>= 2) MD5sum: 3bd06614e7ef1830218daf39c3bdc276 NeedsCompilation: yes Package: AffyRNADegradation Version: 1.44.0 Depends: R (>= 2.9.0), methods, affy Suggests: AmpAffyExample License: GPL-2 MD5sum: 0a1d2444de49c7558c377344a93490a3 NeedsCompilation: no Package: AGDEX Version: 1.46.0 Depends: R (>= 2.10), Biobase, GSEABase Imports: stats License: GPL (>= 2) MD5sum: 394c9e162d25b5506048cc9eb071a49e NeedsCompilation: no Package: aggregateBioVar Version: 1.8.0 Depends: R (>= 4.0) Imports: stats, methods, S4Vectors, SummarizedExperiment, SingleCellExperiment, Matrix, tibble, rlang Suggests: BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics, DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext, RColorBrewer, pheatmap, viridis License: GPL-3 MD5sum: 42b7169cc0f2bd5dc0d8e25bfde7ae6c NeedsCompilation: no Package: agilp Version: 3.30.0 Depends: R (>= 2.14.0) License: GPL-3 MD5sum: b1cbcf2d05504173f46361abad2d9c2b NeedsCompilation: no Package: AgiMicroRna Version: 2.48.0 Depends: R (>= 2.10),methods,Biobase,limma,affy (>= 1.22),preprocessCore,affycoretools Imports: Biobase Suggests: geneplotter,marray,gplots,gtools,gdata,codelink License: GPL-3 MD5sum: 2e41a1337e2cab4d4e7b07bed6eef408 NeedsCompilation: no Package: AIMS Version: 1.30.0 Depends: R (>= 2.10), e1071, Biobase Suggests: breastCancerVDX, hgu133a.db, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 1d11f0658be529942cf9ecb580295308 NeedsCompilation: no Package: airpart Version: 1.6.0 Depends: R (>= 4.1) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, scater, stats, smurf, apeglm (>= 1.13.3), emdbook, mclust, clue, dynamicTreeCut, matrixStats, dplyr, plyr, ggplot2, ComplexHeatmap, forestplot, RColorBrewer, rlang, lpSolve, grid, grDevices, graphics, utils, pbapply Suggests: knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0), gplots, tidyr License: GPL-2 MD5sum: 47bc2fead61ca20f0852ef3c27b9d0fe NeedsCompilation: no Package: ALDEx2 Version: 1.30.0 Depends: methods, stats, zCompositions, Imports: Rfast, BiocParallel, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, multtest Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 3) MD5sum: 176a430e5a6cf5da2530c59ee4f69fbf NeedsCompilation: no Package: alevinQC Version: 1.14.0 Depends: R (>= 4.0) Imports: rmarkdown (>= 2.5), tools, methods, ggplot2, GGally, dplyr, rjson, shiny, shinydashboard, DT, stats, utils, tximport (>= 1.17.4), cowplot, rlang, Rcpp LinkingTo: Rcpp Suggests: knitr, BiocStyle, testthat (>= 3.0.0), BiocManager License: MIT + file LICENSE MD5sum: 729a1c1fe011e289cfc10b91f1ecf27b NeedsCompilation: yes Package: AllelicImbalance Version: 1.36.0 Depends: R (>= 4.0.0), grid, GenomicRanges (>= 1.31.8), SummarizedExperiment (>= 0.2.0), GenomicAlignments (>= 1.15.6) Imports: methods, BiocGenerics, AnnotationDbi, BSgenome (>= 1.47.3), VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Rsamtools (>= 1.99.3), GenomicFeatures (>= 1.31.3), Gviz, lattice, latticeExtra, gridExtra, seqinr, GenomeInfoDb, nlme Suggests: testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: ad27098a91fbd7d356d46cd43d7a2af0 NeedsCompilation: no Package: AlphaBeta Version: 1.12.0 Depends: R (>= 3.6.0) Imports: dplyr (>= 0.7), data.table (>= 1.10), stringr (>= 1.3), utils (>= 3.6.0), gtools (>= 3.8.0), optimx (>= 2018-7.10), expm (>= 0.999-4), stats (>= 3.6), BiocParallel (>= 1.18), igraph (>= 1.2.4), graphics (>= 3.6), ggplot2 (>= 3.2), grDevices (>= 3.6), plotly (>= 4.9) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 2822aaf9b95e6ef87dbf7f28931009d1 NeedsCompilation: no Package: alpine Version: 1.24.0 Depends: R (>= 3.5.0) Imports: Biostrings, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, SummarizedExperiment, GenomicFeatures, speedglm, splines, graph, RBGL, stringr, stats, methods, graphics, GenomeInfoDb, S4Vectors Suggests: knitr, testthat, markdown, alpineData, rtracklayer, ensembldb, BSgenome.Hsapiens.NCBI.GRCh38, RColorBrewer License: GPL (>= 2) MD5sum: 5e808fea76aa64d1b4188fadbd2055e0 NeedsCompilation: no Package: AlpsNMR Version: 4.0.4 Depends: R (>= 4.2), future (>= 1.10.0) Imports: utils, generics, graphics, stats, grDevices, cli, magrittr (>= 1.5), dplyr (>= 1.1.0), signal (>= 0.7-6), rlang (>= 0.3.0.1), scales (>= 1.2.0), stringr (>= 1.3.1), tibble(>= 1.3.4), tidyr (>= 1.0.0), tidyselect, readxl (>= 1.1.0), purrr (>= 0.2.5), glue (>= 1.2.0), reshape2 (>= 1.4.3), mixOmics (>= 6.3.2), matrixStats (>= 0.54.0), fs (>= 1.2.6), rmarkdown (>= 1.10), speaq (>= 2.4.0), htmltools (>= 0.3.6), pcaPP (>= 1.9-73), ggplot2 (>= 3.1.0), baseline (>= 1.2-1), vctrs (>= 0.3.0), BiocParallel Suggests: BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5), GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr, plotly (>= 4.7.1), progressr, SummarizedExperiment, S4Vectors, testthat (>= 2.0.0), writexl (>= 1.0), zip (>= 2.0.4) License: MIT + file LICENSE MD5sum: 5afcd910f5242bde6a3e2f92bcb60600 NeedsCompilation: no Package: altcdfenvs Version: 2.60.0 Depends: R (>= 2.7), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.9.25), Biobase (>= 2.15.1), affy, makecdfenv, Biostrings, hypergraph Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer License: GPL (>= 2) MD5sum: 314a03730c8948d9da6c351f356135fc NeedsCompilation: no Package: AMARETTO Version: 1.14.0 Depends: R (>= 3.6), impute, doParallel, grDevices, dplyr, methods, ComplexHeatmap Imports: callr (>= 3.0.0.9001), Matrix, Rcpp, BiocFileCache, DT, MultiAssayExperiment, circlize, curatedTCGAData, foreach, glmnet, httr, limma, matrixStats, readr, reshape2, tibble, rmarkdown, graphics, grid, parallel, stats, knitr, ggplot2, gridExtra, utils LinkingTo: Rcpp Suggests: testthat, MASS, knitr License: Apache License (== 2.0) + file LICENSE MD5sum: aa87962f7524e66e90c8e41da55d28c5 NeedsCompilation: no Package: AMOUNTAIN Version: 1.24.0 Depends: R (>= 3.3.0) Imports: stats Suggests: BiocStyle, qgraph, knitr, rmarkdown License: GPL (>= 2) MD5sum: dc945636cf4935aecde8f0a309be8ada NeedsCompilation: yes Package: amplican Version: 1.20.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.22.0), Biostrings (>= 2.44.2), data.table (>= 1.10.4-3) Imports: Rcpp, utils (>= 3.4.1), S4Vectors (>= 0.14.3), ShortRead (>= 1.34.0), IRanges (>= 2.10.2), GenomicRanges (>= 1.28.4), GenomeInfoDb (>= 1.12.2), BiocParallel (>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 2.2.0), ggthemes (>= 3.4.0), waffle (>= 0.7.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), dplyr (>= 0.7.2), rmarkdown (>= 1.6), knitr (>= 1.16), clusterCrit (>= 1.2.7) LinkingTo: Rcpp Suggests: testthat, BiocStyle, GenomicAlignments License: GPL-3 MD5sum: b8bc391abea8de9e3a3659ff29374379 NeedsCompilation: yes Package: Anaquin Version: 2.22.0 Depends: R (>= 3.3), ggplot2 (>= 2.2.0) Imports: ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils, plyr, DESeq2 Suggests: RUnit, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 3918e7fad4663db676e6df169bed2ba5 NeedsCompilation: no Package: ANCOMBC Version: 2.0.2 Depends: R (>= 4.2.0) Imports: mia, stats, CVXR, DescTools, Hmisc, MASS, Rdpack, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, doParallel, doRNG, dplyr, emmeans, energy, foreach, lme4, lmerTest, magrittr, nloptr, parallel, rlang, rngtools, tibble, tidyr, utils Suggests: knitr, rmarkdown, testthat, DT, caret, microbiome, tidyverse License: Artistic-2.0 MD5sum: da2398479411b5dfd6ee8ade6908b19d NeedsCompilation: no Package: AneuFinder Version: 1.26.0 Depends: R (>= 3.5), GenomicRanges, ggplot2, cowplot, AneuFinderData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, Rsamtools, bamsignals, DNAcopy, ecp, Biostrings, GenomicAlignments, reshape2, ggdendro, ggrepel, ReorderCluster, mclust Suggests: knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: ad1d7408f9f3558fadbf40f18fae9bbd NeedsCompilation: yes Package: ANF Version: 1.20.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 MD5sum: a67284ce5d09605d7752ca1386617428 NeedsCompilation: no Package: animalcules Version: 1.14.0 Depends: R (>= 4.0.0) Imports: assertthat, shiny, shinyjs, DESeq2, caret, plotly, ggplot2, rentrez, reshape2, covr, ape, vegan, dplyr, magrittr, MultiAssayExperiment, SummarizedExperiment, S4Vectors (>= 0.23.19), XML, forcats, scales, lattice, glmnet, tsne, plotROC, DT, utils, limma, methods, stats, tibble, biomformat, umap, Matrix, GUniFrac Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 9350e28f5ac8d04f6109c49c5fe1eee3 NeedsCompilation: no Package: annaffy Version: 1.70.0 Depends: R (>= 2.5.0), methods, Biobase, BiocManager, GO.db Imports: AnnotationDbi (>= 0.1.15), DBI Suggests: hgu95av2.db, multtest, tcltk License: LGPL MD5sum: 9f5252619c2fb8cf2ca23b705af46aab NeedsCompilation: no Package: annmap Version: 1.40.0 Depends: R (>= 2.15.0), methods, GenomicRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice, Rsamtools, genefilter, IRanges, BiocGenerics Suggests: RUnit, rjson, Gviz License: GPL-2 MD5sum: a2475106a6afb06daff638379e97d869 NeedsCompilation: no Package: annotate Version: 1.76.0 Depends: R (>= 2.10), AnnotationDbi (>= 1.27.5), XML Imports: Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), httr Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, License: Artistic-2.0 MD5sum: 8e3f53138dee78c278c5181d14579ef3 NeedsCompilation: no Package: AnnotationDbi Version: 1.60.2 Depends: R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges Imports: DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST Suggests: hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 MD5sum: f4a6607e3a70381e5daa861e60a4c0fe NeedsCompilation: no Package: AnnotationFilter Version: 1.22.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown License: Artistic-2.0 MD5sum: 479cc3a2941b020e86b344ee1fc49597 NeedsCompilation: no Package: AnnotationForge Version: 1.40.2 Depends: R (>= 3.5.0), methods, utils, BiocGenerics (>= 0.15.10), Biobase (>= 1.17.0), AnnotationDbi (>= 1.33.14) Imports: DBI, RSQLite, XML, S4Vectors, RCurl Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, markdown, BiocStyle, knitr, BiocManager, BiocFileCache License: Artistic-2.0 MD5sum: ffe79c46d29549916e65ca5813567d28 NeedsCompilation: no Package: AnnotationHub Version: 3.6.0 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, interactiveDisplayBase, httr, yaml, dplyr Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 0cf4c3b511b29d9375eed93381239b76 NeedsCompilation: yes Package: AnnotationHubData Version: 1.28.0 Depends: R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges (>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15) Imports: GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocManager, biocViews, BiocCheck, graph, AnnotationDbi, Biobase, Biostrings, DBI, GenomeInfoDb (>= 1.15.4), OrganismDbi, RSQLite, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub License: Artistic-2.0 MD5sum: 426aaaf49408beb78eea1f1d09428fbd NeedsCompilation: no Package: annotationTools Version: 1.72.0 Imports: Biobase, stats Suggests: BiocStyle License: GPL MD5sum: cb3cd53a81f8ebc598cb5e95cf41c3a3 NeedsCompilation: no Package: annotatr Version: 1.24.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures, GenomicRanges, GenomeInfoDb (>= 1.10.3), ggplot2, IRanges, methods, readr, regioneR, reshape2, rtracklayer, S4Vectors (>= 0.23.10), stats, utils Suggests: BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene License: GPL-3 MD5sum: 7baf3ac4f6a76c7c09caff7fef435d08 NeedsCompilation: no Package: anota Version: 1.46.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: 3d3e04a8fb10434fb98e3026a5cb4943 NeedsCompilation: no Package: anota2seq Version: 1.20.0 Depends: R (>= 3.4.0), methods Imports: multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices, graphics, stats, utils, SummarizedExperiment Suggests: BiocStyle,knitr License: GPL-3 MD5sum: f9e143aea5e03df220d16c65e5ecb984 NeedsCompilation: no Package: antiProfiles Version: 1.38.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: cc00a140351e3f2dfaa0a5ea88f9eb84 NeedsCompilation: no Package: AnVIL Version: 1.10.2 Depends: R (>= 3.6), dplyr Imports: stats, utils, methods, futile.logger, jsonlite, httr, rapiclient (>= 0.1.3), tibble, tidyselect, tidyr, rlang, shiny, DT, miniUI, htmltools, BiocManager Suggests: parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools License: Artistic-2.0 MD5sum: 50b0905bc683515b13c32996f0ccdede NeedsCompilation: no Package: AnVILBilling Version: 1.8.0 Depends: R (>= 4.1) Imports: methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr, dplyr, lubridate, plotly, ggplot2 Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: e7db4f23c6f10a0aa48289d99d4700d0 NeedsCompilation: no Package: AnVILPublish Version: 1.8.0 Imports: AnVIL, httr, jsonlite, rmarkdown, yaml, readr, whisker, tools, utils, stats Suggests: knitr, BiocStyle, BiocManager, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 73c4909afcf29b2ac9d08a22dc932632 NeedsCompilation: no Package: APAlyzer Version: 1.12.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq2, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, VariantAnnotation, dplyr, tidyr, repmis, Rsamtools, HybridMTest Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset License: LGPL-3 MD5sum: 92d468e84e770089d6d301929a191bec NeedsCompilation: no Package: apComplex Version: 2.64.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: d8fcbf77040efe7bc5dee5bd1e303c57 NeedsCompilation: no Package: apeglm Version: 1.20.0 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 MD5sum: ff2b45cd3e43bfe8f6a4184a1d5ba349 NeedsCompilation: yes Package: APL Version: 1.2.0 Depends: R (>= 4.2) Imports: reticulate, ggrepel, ggplot2, viridisLite, plotly, Seurat, SingleCellExperiment, magrittr, SummarizedExperiment, topGO, methods, stats, utils, org.Hs.eg.db, org.Mm.eg.db, rlang Suggests: BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, testthat License: GPL (>= 3) MD5sum: 642b14abaf442e3724c459a5eebc2956 NeedsCompilation: no Package: appreci8R Version: 1.16.0 Imports: shiny, shinyjs, DT, VariantAnnotation, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, rsnps, Biostrings, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.gnomADex.r2.1.hs37d5, COSMIC.67, rentrez, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137, seqinr, openxlsx, Rsamtools, stringr, utils, stats, GenomicRanges, S4Vectors, GenomicFeatures, IRanges, GenomicScores, SummarizedExperiment Suggests: GO.db, org.Hs.eg.db License: LGPL-3 MD5sum: bf71dc7fbecf1dcd7ed10576d9127458 NeedsCompilation: no Package: aroma.light Version: 3.28.0 Depends: R (>= 2.15.2) Imports: stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.23.0), R.utils (>= 2.9.0), matrixStats (>= 0.55.0) Suggests: princurve (>= 2.1.4) License: GPL (>= 2) MD5sum: 41873cd80a3006a0c1e3d97a5dd41e3f NeedsCompilation: no Package: ArrayExpress Version: 1.57.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: XML, oligo, limma Suggests: affy License: Artistic-2.0 MD5sum: b6acb78969e4a9e0474dbb96fdf1a46f NeedsCompilation: no Package: ArrayExpressHTS Version: 1.47.0 Depends: sampling, Rsamtools (>= 1.99.0), snow Imports: Biobase, BiocGenerics, Biostrings, GenomicRanges, Hmisc, IRanges (>= 2.13.11), R2HTML, RColorBrewer, Rsamtools, ShortRead, XML, biomaRt, edgeR, grDevices, graphics, methods, rJava, stats, svMisc, utils, sendmailR, bitops LinkingTo: Rhtslib (>= 1.15.3) License: Artistic License 2.0 MD5sum: a737adbd619efab5b847cae073a55848 NeedsCompilation: yes Package: arrayMvout Version: 1.56.0 Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy Imports: mdqc, affyContam, lumi Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf License: Artistic-2.0 MD5sum: 2e824877f0535fafa29106d192931e34 NeedsCompilation: no Package: arrayQuality Version: 1.76.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL MD5sum: 0feba15db585d8925f0c25e54751d6a7 NeedsCompilation: no Package: arrayQualityMetrics Version: 3.54.0 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, genefilter, graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, stats, utils, vsn (>= 3.23.3), XML, svglite Suggests: ALLMLL, CCl4, BiocStyle, knitr License: LGPL (>= 2) MD5sum: fbeea53cd5c65f8ccf62c1473e622f89 NeedsCompilation: no Package: ARRmNormalization Version: 1.38.0 Depends: R (>= 2.15.1), ARRmData License: Artistic-2.0 MD5sum: 271de41ca9a42c15860876f8e79836b0 NeedsCompilation: no Package: artMS Version: 1.16.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, bit64, circlize, cluster, corrplot, data.table, dplyr, getopt, ggdendro, ggplot2, gplots, ggrepel, graphics, grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db, pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml Suggests: BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat License: GPL (>= 3) + file LICENSE MD5sum: 2ef02b42db86fef7bad3743456c66688 NeedsCompilation: no Package: ASAFE Version: 1.24.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 46ac15b9109436311f6f5cca89056df4 NeedsCompilation: no Package: ASEB Version: 1.42.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) MD5sum: ec93c088b0d32771d713c713c3bd7e2a NeedsCompilation: yes Package: ASGSCA Version: 1.32.0 Imports: Matrix, MASS Suggests: BiocStyle License: GPL-3 MD5sum: 4b2e5da9da66a109a1e9bb34086044a5 NeedsCompilation: no Package: ASICS Version: 2.14.0 Depends: R (>= 3.5) Imports: BiocParallel, ggplot2, glmnet, grDevices, gridExtra, methods, mvtnorm, PepsNMR, plyr, quadprog, ropls, stats, SummarizedExperiment, utils, Matrix, zoo Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata License: GPL (>= 2) MD5sum: 42618e0ae51c5fb0ad97e5f72bf0b295 NeedsCompilation: no Package: ASpediaFI Version: 1.11.0 Depends: R (>= 3.6.0), SummarizedExperiment, ROCR Imports: BiocParallel, GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges, IVAS, Rsamtools, biomaRt, limma, S4Vectors, stats, DRaWR, GenomeInfoDb, Gviz, Matrix, dplyr, fgsea, reshape2, igraph, graphics, e1071, methods, rtracklayer, scales, grid, ggplot2, mGSZ, utils Suggests: knitr License: GPL-3 MD5sum: cc09f47446cb09110d4b6889d52c6c14 NeedsCompilation: no Package: ASpli Version: 2.8.0 Depends: methods, grDevices, stats, utils, parallel, edgeR, limma, AnnotationDbi Imports: GenomicRanges, GenomicFeatures, BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, Rsamtools, BiocStyle, igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid, graphics, pbmcapply License: GPL MD5sum: 0b44adbcd9b1533799a07ca9082eb239 NeedsCompilation: no Package: AssessORF Version: 1.16.0 Depends: R (>= 3.5.0), DECIPHER (>= 2.10.0) Imports: Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: c1f8a5e955f04bf92610e1b75551a330 NeedsCompilation: no Package: ASSET Version: 2.16.0 Depends: R (>= 3.5.0), stats, graphics Imports: MASS, msm, rmeta Suggests: RUnit, BiocGenerics, knitr License: GPL-2 + file LICENSE MD5sum: f6009892f7d3840dbd00a55cbee23627 NeedsCompilation: no Package: ASSIGN Version: 1.34.0 Depends: R (>= 3.4) Imports: gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 90043100613f938ff0a7bf54c9288285 NeedsCompilation: no Package: ASURAT Version: 1.2.0 Depends: R (>= 4.0.0) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp (>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize, grid, grDevices, graphics LinkingTo: Rcpp Suggests: ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: e8f11759f0e72d7504f271e8de82388e NeedsCompilation: yes Package: ATACCoGAPS Version: 1.0.0 Depends: R (>= 4.2.0), CoGAPS (>= 3.5.13) Imports: gtools, GenomicRanges, projectR, TFBSTools, GeneOverlap, msigdbr, tidyverse, gplots, motifmatchr, chromVAR, GenomicFeatures, IRanges, fgsea, rGREAT, JASPAR2016, Homo.sapiens, Mus.musculus, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, stringr, dplyr Suggests: knitr, viridis License: Artistic-2.0 MD5sum: e1e57847a30aa2a8a5b07cf4513621de NeedsCompilation: no Package: ATACseqQC Version: 1.22.0 Depends: R (>= 3.5.0), BiocGenerics, S4Vectors Imports: BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats, motifStack, preseqR, utils, KernSmooth, edgeR Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown License: GPL (>= 2) MD5sum: 7c486d6bc3730cc9bb1a12601f6d4733 NeedsCompilation: no Package: ATACseqTFEA Version: 1.0.1 Depends: R (>= 4.2) Imports: BiocGenerics, S4Vectors, IRanges, Matrix, GenomicRanges, GenomicAlignments, GenomeInfoDb, SummarizedExperiment, Rsamtools, motifmatchr, TFBSTools, stats, pracma, ggplot2, ggrepel, dplyr, limma, methods Suggests: BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle License: GPL-3 MD5sum: e5de11a5adccff977b830f09981cca58 NeedsCompilation: no Package: atena Version: 1.4.1 Depends: R (>= 4.1), SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, BiocParallel, S4Vectors, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, scales, matrixStats Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: ae24e1475f76c875e62d5e9bc1b49f2b NeedsCompilation: no Package: atSNP Version: 1.14.0 Depends: R (>= 3.6) Imports: BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testthat, utils, lifecycle LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 369b51757f87d6aa9db6525362ff0ff8 NeedsCompilation: yes Package: attract Version: 1.50.0 Depends: R (>= 3.4.0), AnnotationDbi Imports: Biobase, limma, cluster, GOstats, graphics, stats, reactome.db, KEGGREST, org.Hs.eg.db, utils, methods Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) MD5sum: cc6d8ec12476dba5e4299fc998cb7e65 NeedsCompilation: no Package: AUCell Version: 1.20.2 Imports: DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, shiny, stats, SummarizedExperiment, BiocGenerics, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, rbokeh, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: 7ca6f285de6793d2b0f538cb57560a99 NeedsCompilation: no Package: autonomics Version: 1.6.0 Depends: R (>= 4.0) Imports: abind, assertive, BiocFileCache, BiocGenerics, colorspace, data.table, edgeR, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma, magrittr, matrixStats, methods, MultiAssayExperiment, parallel, pcaMethods, rappdirs, rlang, R.utils, readxl, S4Vectors, scales, stats, stringi, SummarizedExperiment, tidyr, tools, utils Suggests: affy, AnnotationDbi, BiocManager, diagram, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, knitr, lme4, lmerTest, MASS, mixOmics, mpm, nlme, org.Hs.eg.db, org.Mm.eg.db, RCurl, remotes, rmarkdown, ropls, Rsubread, rtracklayer, seqinr, statmod, testthat License: GPL-3 MD5sum: 10dfc68a0d084e41156bd314c28fc5b8 NeedsCompilation: no Package: AWFisher Version: 1.12.0 Depends: R (>= 3.6) Imports: edgeR, limma, stats Suggests: knitr, tightClust License: GPL-3 MD5sum: f00e62ecac272132a25beb2b8408b2c9 NeedsCompilation: yes Package: awst Version: 1.6.0 Imports: stats, methods, SummarizedExperiment Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown License: MIT + file LICENSE MD5sum: 294622a361a7c2462c8c71c2b60d8105 NeedsCompilation: no Package: BaalChIP Version: 1.24.0 Depends: R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools, Imports: GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy, reshape2, scales, coda, foreach, ggplot2, methods, utils, graphics, stats Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 933d1b8c39f86e9b5804d12fde54fe99 NeedsCompilation: no Package: BAC Version: 1.58.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: e2e16f6a6fdcea62f2c81fa22b028c1a NeedsCompilation: yes Package: bacon Version: 1.26.0 Depends: R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 License: GPL (>= 2) MD5sum: 6e3160f5907ac61082baa9c6f98002a4 NeedsCompilation: yes Package: BADER Version: 1.36.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 MD5sum: 712d02420f6824e3e537e5a2af245401 NeedsCompilation: yes Package: BadRegionFinder Version: 1.26.0 Imports: VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: ff6406ba94601dea34f2ae0d8818213b NeedsCompilation: no Package: BAGS Version: 2.38.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 MD5sum: 2a843ff3165670ae6de5872a349b0f10 NeedsCompilation: yes Package: ballgown Version: 2.30.0 Depends: R (>= 3.5.0), methods Imports: GenomicRanges (>= 1.17.25), IRanges (>= 1.99.22), S4Vectors (>= 0.9.39), RColorBrewer, splines, sva, limma, rtracklayer (>= 1.29.25), Biobase (>= 2.25.0), GenomeInfoDb Suggests: testthat, knitr, markdown License: Artistic-2.0 MD5sum: f852baa110225bc98fb910e57cdd8638 NeedsCompilation: no Package: bambu Version: 3.0.8 Depends: R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>= 0.22.1), BSgenome, IRanges Imports: BiocGenerics, BiocParallel, data.table, dplyr, tidyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost LinkingTo: Rcpp, RcppArmadillo Suggests: AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq Enhances: parallel License: GPL-3 + file LICENSE MD5sum: 69b4a8c169e891cab62fcac39a20c9cf NeedsCompilation: yes Package: bamsignals Version: 1.30.0 Depends: R (>= 3.5.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 15da3cbccec7fa05126994cd29321527 NeedsCompilation: yes Package: BANDITS Version: 1.14.2 Depends: R (>= 4.0.0) Imports: Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings License: GPL (>= 3) MD5sum: 8bb204aa5cd45961aecb107b00599a40 NeedsCompilation: yes Package: bandle Version: 1.2.2 Depends: R (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc Imports: Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr, knitr, methods, BiocParallel, robustbase, BiocStyle, ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils, grDevices, rlang LinkingTo: Rcpp, RcppArmadillo, BH Suggests: coda (>= 0.19-4), testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling License: Artistic-2.0 MD5sum: bd379edc3c92e9fff1b21c92949ed82e NeedsCompilation: yes Package: banocc Version: 1.22.0 Depends: R (>= 3.5.1), rstan (>= 2.17.4) Imports: coda (>= 0.18.1), mvtnorm, stringr Suggests: knitr, rmarkdown, methods, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 892551c4602b33cb7cc06eee2e2d1265 NeedsCompilation: no Package: barcodetrackR Version: 1.6.0 Depends: R (>= 4.1) Imports: cowplot, circlize, dplyr, ggplot2, ggdendro, ggridges, graphics, grDevices, magrittr, plyr, proxy, RColorBrewer, rlang, scales, shiny, stats, SummarizedExperiment, S4Vectors, tibble, tidyr, vegan, viridis, utils Suggests: BiocStyle, knitr, magick, rmarkdown, testthat License: file LICENSE MD5sum: 0928f60a14c5428b02f1ce9e38220799 NeedsCompilation: no Package: basecallQC Version: 1.22.0 Depends: R (>= 3.4), stats, utils, methods, rmarkdown, knitr, prettydoc, yaml Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead Suggests: testthat, BiocStyle License: GPL (>= 3) MD5sum: 8c535ac5b437b427c2faa253f1438034 NeedsCompilation: no Package: BaseSpaceR Version: 1.42.0 Depends: R (>= 2.15.0), RCurl, RJSONIO Imports: methods Suggests: RUnit, IRanges, Rsamtools License: Apache License 2.0 MD5sum: 37384bb87932e9fa40ec827c9630061f NeedsCompilation: no Package: Basic4Cseq Version: 1.34.0 Depends: R (>= 3.4), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805 Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: f765d73bd452b6d36dc9ad94d9867ef0 NeedsCompilation: no Package: BASiCS Version: 2.10.5 Depends: R (>= 4.0), SingleCellExperiment Imports: Biobase, BiocGenerics, coda, cowplot, ggExtra, ggplot2, graphics, grDevices, MASS, methods, Rcpp (>= 0.11.3), S4Vectors, scran, scuttle, stats, stats4, SummarizedExperiment, viridis, utils, Matrix (>= 1.5.0), matrixStats, assertthat, reshape2, BiocParallel, hexbin LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, magick License: GPL (>= 2) MD5sum: 27fd2ffad9308d17edac943f272641f0 NeedsCompilation: yes Package: BASiCStan Version: 1.0.0 Depends: R (>= 4.2), BASiCS, rstan (>= 2.18.1) Imports: methods, glmGamPoi, scran, scuttle, stats, utils, SingleCellExperiment, SummarizedExperiment, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstantools (>= 2.1.1) LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 MD5sum: d7a579460820805e68fc5d9565af5ba1 NeedsCompilation: yes Package: BasicSTARRseq Version: 1.26.0 Depends: GenomicRanges,GenomicAlignments Imports: S4Vectors,methods,IRanges,GenomeInfoDb,stats Suggests: knitr License: LGPL-3 MD5sum: 9717c2f5eaf1792c629a637e971f2bd3 NeedsCompilation: no Package: basilisk Version: 1.10.2 Imports: utils, methods, parallel, reticulate, dir.expiry, basilisk.utils Suggests: knitr, rmarkdown, BiocStyle, testthat, callr License: GPL-3 MD5sum: 5844a4062e45b474042a68f37fca5425 NeedsCompilation: no Package: basilisk.utils Version: 1.10.0 Imports: utils, methods, tools, dir.expiry Suggests: reticulate, knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 9e3a4c0ec22a491c0bfb6d7fefbe2587 NeedsCompilation: no Package: batchelor Version: 1.14.1 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix, DelayedArray, DelayedMatrixStats, BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq License: GPL-3 MD5sum: f8230f96c9f7d0046ea0ee4e7926448e NeedsCompilation: yes Package: BatchQC Version: 1.26.0 Depends: R (>= 3.5.0) Imports: utils, rmarkdown, knitr, pander, gplots, MCMCpack, shiny, sva, corpcor, moments, matrixStats, ggvis, heatmaply, reshape2, limma, grDevices, graphics, stats, methods, Matrix Suggests: testthat License: GPL (>= 2) MD5sum: bb2d42cb4e5cac641e3f9bbc04b9079a NeedsCompilation: no Package: BayesKnockdown Version: 1.24.0 Depends: R (>= 3.3) Imports: stats, Biobase License: GPL-3 MD5sum: 38d94347d31da27b1b3ed63a5833570d NeedsCompilation: no Package: BayesSpace Version: 1.8.2 Depends: R (>= 4.0.0), SingleCellExperiment Imports: Rcpp (>= 1.0.4.6), stats, purrr, scater, scran, SummarizedExperiment, coda, rhdf5, S4Vectors, Matrix, assertthat, mclust, RCurl, DirichletReg, xgboost, utils, ggplot2, scales, BiocFileCache, BiocSingular LinkingTo: Rcpp, RcppArmadillo, RcppDist, RcppProgress Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, dplyr, viridis, patchwork, RColorBrewer, Seurat License: MIT + file LICENSE MD5sum: 5675845abc284d10d8595a2aeed4b88c NeedsCompilation: yes Package: bayNorm Version: 1.16.2 Depends: R (>= 3.5), Imports: Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix, parallel, MASS, locfit, fitdistrplus, stats, methods, graphics, grDevices, SingleCellExperiment, SummarizedExperiment, BiocParallel, utils LinkingTo: Rcpp, RcppArmadillo,RcppProgress Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat License: GPL (>= 2) MD5sum: 5bb0855e7bbde18de4a283aac8d9d2de NeedsCompilation: yes Package: baySeq Version: 2.31.0 Depends: R (>= 2.3.0), methods, GenomicRanges, abind, parallel Imports: edgeR Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: 7190586dd45adb3d81d58b3e22ebd0e1 NeedsCompilation: no Package: BBCAnalyzer Version: 1.28.0 Imports: SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices, GenomicRanges, IRanges, Biostrings Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 4ab38c1b5062a171b4f522791f6b172f NeedsCompilation: no Package: BCRANK Version: 1.60.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 MD5sum: c3494f9c7ec4b41596d1b3132005c0c7 NeedsCompilation: yes Package: bcSeq Version: 1.20.0 Depends: R (>= 3.4.0) Imports: Rcpp (>= 0.12.12), Matrix, Biostrings LinkingTo: Rcpp, Matrix Suggests: knitr License: GPL (>= 2) MD5sum: ed0791e7abeeb2b460788ae18b00e33d NeedsCompilation: yes Package: BDMMAcorrect Version: 1.16.2 Depends: R (>= 3.5), vegan, ellipse, ggplot2, ape, SummarizedExperiment Imports: Rcpp (>= 0.12.12), RcppArmadillo, RcppEigen, stats LinkingTo: Rcpp, RcppArmadillo, RcppEigen Suggests: knitr, rmarkdown, BiocGenerics License: GPL (>= 2) MD5sum: 91bbe0bc98938b15b46d51d53831666c NeedsCompilation: yes Package: beachmat Version: 2.14.2 Imports: methods, DelayedArray (>= 0.15.14), BiocGenerics, Matrix, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array License: GPL-3 MD5sum: 32e51c014f2113a5f2574df224d86d36 NeedsCompilation: yes Package: beadarray Version: 2.48.0 Depends: R (>= 2.13.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), hexbin Imports: BeadDataPackR, limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, illuminaio, methods, ggplot2 Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr License: MIT + file LICENSE MD5sum: 5e7875372002d464edbd50a0730ef127 NeedsCompilation: yes Package: beadarraySNP Version: 1.64.0 Depends: methods, Biobase (>= 2.14), quantsmooth Suggests: aCGH, affy, limma, snapCGH, beadarray, DNAcopy License: GPL-2 MD5sum: 93d114478e3d57db6f8d64308c0ee93d NeedsCompilation: no Package: BeadDataPackR Version: 1.50.0 Imports: stats, utils Suggests: BiocStyle, knitr License: GPL-2 MD5sum: 956d16e2749f7236da3d7e52f987b5a5 NeedsCompilation: yes Package: BEARscc Version: 1.18.0 Depends: R (>= 3.5.0) Imports: ggplot2, SingleCellExperiment, data.table, stats, utils, graphics, compiler Suggests: testthat, cowplot, knitr, rmarkdown, BiocStyle, NMF License: GPL-3 MD5sum: 4225cd3708a3e94b611f12d829b82b97 NeedsCompilation: no Package: BEAT Version: 1.36.0 Depends: R (>= 2.13.0) Imports: GenomicRanges, ShortRead, Biostrings, BSgenome License: LGPL (>= 3.0) MD5sum: aaa68971dad49206a5dcfca6df94f39e NeedsCompilation: no Package: BEclear Version: 2.14.0 Depends: BiocParallel (>= 1.14.2) Imports: futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp, abind, stats, graphics, utils, methods, dixonTest, ids LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, pander, seewave License: GPL-3 MD5sum: 77cc95ab6af022a293812f58a9cb164d NeedsCompilation: yes Package: beer Version: 1.2.0 Depends: R (>= 4.2.0), PhIPData (>= 1.1.1), rjags Imports: cli, edgeR, BiocParallel, methods, progressr, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling License: MIT + file LICENSE MD5sum: 60b21cf6d049865d7a2cd0517edcc7de NeedsCompilation: no Package: benchdamic Version: 1.4.0 Depends: R (>= 4.2.0) Imports: stats, stats4, utils, methods, phyloseq, TreeSummarizedExperiment, BiocParallel, zinbwave, edgeR, DESeq2, limma, ALDEx2, SummarizedExperiment, MAST, Seurat, ANCOMBC, NOISeq, dearseq, metagenomeSeq, corncob, MGLM, ggplot2, RColorBrewer, plyr, reshape2, ggdendro, ggridges, graphics, cowplot, tidytext Suggests: knitr, rmarkdown, kableExtra, BiocStyle, SPsimSeq, testthat License: Artistic-2.0 MD5sum: 7e36d2d9efd63244c15e67bd564d0f29 NeedsCompilation: no Package: BgeeCall Version: 1.14.0 Depends: R (>= 3.6) Imports: GenomicFeatures, tximport, Biostrings, rtracklayer, biomaRt, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5 Suggests: knitr, testthat, rmarkdown, AnnotationHub, httr License: GPL-3 + file LICENSE MD5sum: a0b4e7b812feb24faaed468efff45fc0 NeedsCompilation: no Package: BgeeDB Version: 2.24.0 Depends: R (>= 3.6.0), topGO, tidyr Imports: R.utils, data.table, curl, RCurl, digest, methods, stats, utils, dplyr, RSQLite, graph, Biobase Suggests: knitr, BiocStyle, testthat, rmarkdown, markdown License: GPL-3 + file LICENSE MD5sum: 58c55b02e47352432b74bc6952b1494e NeedsCompilation: no Package: BGmix Version: 1.58.0 Depends: R (>= 2.3.1), KernSmooth License: GPL-2 MD5sum: f5ddae2d1fd13e1bc75d01e5fe25ebce NeedsCompilation: yes Package: bgx Version: 1.64.0 Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), gcrma (>= 2.4.1) Imports: Rcpp (>= 0.11.0) LinkingTo: Rcpp Suggests: affydata, hgu95av2cdf License: GPL-2 MD5sum: cd8efcdeb0169ceb0c59ed8e05ae46e4 NeedsCompilation: yes Package: BHC Version: 1.50.0 License: GPL-3 MD5sum: 96aa50b1c7ae1198f5c1431ca9ec0139 NeedsCompilation: yes Package: BicARE Version: 1.56.0 Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase License: GPL-2 MD5sum: c2a2edf555aff1e3753cafef7b52fb1a NeedsCompilation: yes Package: BiFET Version: 1.18.0 Depends: R (>= 3.5.0) Imports: stats, poibin, GenomicRanges Suggests: rmarkdown, testthat, knitr License: GPL-3 MD5sum: 7bd7c7d5b809fc67e4366adc10fdb8f3 NeedsCompilation: no Package: BiGGR Version: 1.34.0 Depends: R (>= 2.14.0), rsbml, hyperdraw, LIM,stringr Imports: hypergraph, limSolve License: file LICENSE MD5sum: 710994f31ca3e07167d94fed4b5e2a8c NeedsCompilation: no Package: bigmelon Version: 1.24.0 Depends: R (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4), methods, minfi (>= 1.21.0), Biobase, methylumi Imports: stats, utils, GEOquery, graphics, BiocGenerics, illuminaio Suggests: BiocGenerics, RUnit, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter License: GPL-3 MD5sum: 8730bb44babecbfa93418203fd947c6b NeedsCompilation: no Package: bigPint Version: 1.14.0 Depends: R (>= 3.6.0) Imports: DelayedArray (>= 0.12.2), dplyr (>= 0.7.2), GGally (>= 1.3.2), ggplot2 (>= 2.2.1), graphics (>= 3.5.0), grDevices (>= 3.5.0), grid (>= 3.5.0), gridExtra (>= 2.3), hexbin (>= 1.27.1), Hmisc (>= 4.0.3), htmlwidgets (>= 0.9), methods (>= 3.5.2), plotly (>= 4.7.1), plyr (>= 1.8.4), RColorBrewer (>= 1.1.2), reshape (>= 0.8.7), shiny (>= 1.0.5), shinycssloaders (>= 0.2.0), shinydashboard (>= 0.6.1), stats (>= 3.5.0), stringr (>= 1.3.1), SummarizedExperiment (>= 1.16.1), tidyr (>= 0.7.0), utils (>= 3.5.0) Suggests: BiocGenerics (>= 0.29.1), data.table (>= 1.11.8), EDASeq (>= 2.14.0), edgeR (>= 3.22.2), gtools (>= 3.5.0), knitr (>= 1.13), matrixStats (>= 0.53.1), rmarkdown (>= 1.10), roxygen2 (>= 3.0.0), RUnit (>= 0.4.32), tibble (>= 1.4.2), License: GPL-3 MD5sum: 65d21bef23c46b5574ccad1ad24313fd NeedsCompilation: no Package: BindingSiteFinder Version: 1.4.0 Depends: GenomicRanges, R (>= 4.2) Imports: tidyr, tibble, dplyr, plyr, matrixStats, stats, ggplot2, methods, rtracklayer, S4Vectors, ggforce, GenomeInfoDb, Gviz Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, ComplexHeatmap, forcats, scales License: Artistic-2.0 MD5sum: 52deafdb0aafe75d1f194464a71549a4 NeedsCompilation: no Package: bioassayR Version: 1.36.0 Depends: R (>= 3.5.0), DBI (>= 0.3.1), RSQLite (>= 1.0.0), methods, Matrix, rjson, BiocGenerics (>= 0.13.8) Imports: XML, ChemmineR Suggests: BiocStyle, RCurl, biomaRt, cellHTS2, knitr, knitcitations, knitrBootstrap, testthat, ggplot2, rmarkdown License: Artistic-2.0 MD5sum: 0ab2c2a602f1e8606e530a2b8b0cafd5 NeedsCompilation: no Package: Biobase Version: 2.58.0 Depends: R (>= 2.10), BiocGenerics (>= 0.27.1), utils Imports: methods Suggests: tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr License: Artistic-2.0 MD5sum: 1590e59da0ac37aa41778c4606c78cf3 NeedsCompilation: yes Package: biobroom Version: 1.30.0 Depends: R (>= 3.0.0), broom Imports: dplyr, tidyr, Biobase Suggests: limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, rmarkdown, SummarizedExperiment License: LGPL MD5sum: 4e6af48650fc1466461a42e8d3e998c8 NeedsCompilation: no Package: biobtreeR Version: 1.10.0 Imports: httr, httpuv, stringi,jsonlite,methods,utils Suggests: BiocStyle, knitr,testthat,rmarkdown,markdown License: MIT + file LICENSE MD5sum: b2710bec73234c23adbcfa5342d15f5c NeedsCompilation: no Package: bioCancer Version: 1.26.04 Depends: R (>= 3.6.0), radiant.data (>= 0.9.1), XML(>= 3.98) Imports: R.oo, httr, DT (>= 0.3), dplyr (>= 0.7.2), shiny (>= 1.0.5), AnnotationDbi, methods, Biobase, geNetClassifier, org.Hs.eg.db, DOSE, clusterProfiler, reactome.db, ReactomePA, DiagrammeR(<= 1.01), visNetwork, htmlwidgets, plyr, tibble Suggests: BiocStyle, prettydoc, rmarkdown, knitr, testthat (>= 0.10.0) License: AGPL-3 | file LICENSE MD5sum: ca87b9777ddfa6dc66dc0f3f6018bebe NeedsCompilation: no Package: BiocBaseUtils Version: 1.0.0 Depends: R (>= 4.2.0) Imports: methods, utils Suggests: knitr, rmarkdown, BiocStyle, tinytest License: Artistic-2.0 MD5sum: 21d78a98e04513a6fc4d827b62d4f27c NeedsCompilation: no Package: BiocCheck Version: 1.34.3 Depends: R (>= 4.2.0) Imports: biocViews (>= 1.33.7), BiocManager, stringdist, graph, httr, tools, codetools, methods, utils, knitr Suggests: RUnit, BiocGenerics, Biobase, jsonlite, rmarkdown, downloader, devtools (>= 1.4.1), usethis, BiocStyle, callr Enhances: codetoolsBioC License: Artistic-2.0 MD5sum: 2866b56dceebae29f889f435eca42a4c NeedsCompilation: no Package: BiocDockerManager Version: 1.10.0 Depends: R (>= 4.1) Imports: httr, whisker, readr, dplyr, utils, methods, memoise Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0) License: Artistic-2.0 MD5sum: 0c2b72ec357a5c718b81882e23bfc2ea NeedsCompilation: no Package: BiocFHIR Version: 1.0.0 Depends: R (>= 4.2) Imports: DT, shiny, jsonlite, graph, tidyr, visNetwork, igraph, utils, methods, BiocBaseUtils Suggests: knitr, testthat, rjsoncons License: Artistic-2.0 MD5sum: 40e5e24e20ae1bfcffc0dddbfcec198a NeedsCompilation: no Package: BiocFileCache Version: 2.6.1 Depends: R (>= 3.4.0), dbplyr (>= 1.0.0) Imports: methods, stats, utils, dplyr, RSQLite, DBI, rappdirs, filelock, curl, httr Suggests: testthat, knitr, BiocStyle, rmarkdown, rtracklayer License: Artistic-2.0 MD5sum: a833918abe25f22c0c82836382027c1a NeedsCompilation: no Package: BiocGenerics Version: 0.44.0 Depends: R (>= 4.0.0), methods, utils, graphics, stats Imports: methods, utils, graphics, stats Suggests: Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray, Biostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase, annotate, RUnit License: Artistic-2.0 MD5sum: 9438855e3f8bb24cecc7588c519ec8dd NeedsCompilation: no Package: biocGraph Version: 1.60.0 Depends: Rgraphviz, graph Imports: Rgraphviz, geneplotter, graph, BiocGenerics, methods Suggests: fibroEset, geneplotter, hgu95av2.db License: Artistic-2.0 MD5sum: 5b20d0b6430960a5202ae6caff59cd89 NeedsCompilation: no Package: BiocIO Version: 1.8.0 Depends: R (>= 4.0) Imports: BiocGenerics, S4Vectors, methods, tools Suggests: testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 11cb131776448affdac365361d827d64 NeedsCompilation: no Package: BiocNeighbors Version: 1.16.0 Imports: Rcpp, S4Vectors, BiocParallel, stats, methods, Matrix LinkingTo: Rcpp, RcppHNSW Suggests: testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW License: GPL-3 MD5sum: 6d64703d14ad67a79306f3ab5f73b8d4 NeedsCompilation: yes Package: BiocOncoTK Version: 1.18.0 Depends: R (>= 3.6.0), methods, utils Imports: ComplexHeatmap, S4Vectors, bigrquery, shiny, stats, httr, rjson, dplyr, magrittr, grid, DT, GenomicRanges, IRanges, ggplot2, SummarizedExperiment, DBI, GenomicFeatures, curatedTCGAData, scales, ggpubr, plyr, car, graph, Rgraphviz Suggests: knitr, dbplyr, org.Hs.eg.db, MultiAssayExperiment, BiocStyle, ontoProc, ontologyPlot, pogos, GenomeInfoDb, restfulSE (>= 1.3.7), BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene, Biobase, TxDb.Hsapiens.UCSC.hg18.knownGene, reshape2, testthat, AnnotationDbi, FDb.InfiniumMethylation.hg19, EnsDb.Hsapiens.v75, rmarkdown, rhdf5client License: Artistic-2.0 MD5sum: 24941b10e4a5813d968e902ee2db5d9f NeedsCompilation: no Package: BioCor Version: 1.22.0 Depends: R (>= 3.4.0) Imports: BiocParallel, GSEABase, Matrix, methods Suggests: airway, BiocStyle, boot, DESeq2, GOSemSim, Hmisc, knitr (>= 1.35), org.Hs.eg.db, reactome.db, rmarkdown, spelling, targetscan.Hs.eg.db, testthat, WGCNA License: MIT + file LICENSE MD5sum: 8bfdf170ccf9c7028c607ed1016d7227 NeedsCompilation: no Package: BiocParallel Version: 1.32.6 Depends: methods, R (>= 3.5.0) Imports: stats, utils, futile.logger, parallel, snow, codetools LinkingTo: BH, cpp11 Suggests: BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel, Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools, data.table License: GPL-2 | GPL-3 MD5sum: 5cfc8676932a40a575f94ebe420c0366 NeedsCompilation: yes Package: BiocPkgTools Version: 1.16.1 Depends: htmlwidgets Imports: BiocFileCache, BiocManager, biocViews, tibble, magrittr, methods, rlang, stringr, rvest, dplyr, xml2, readr, httr, htmltools, DT, tools, utils, igraph, jsonlite, gh, RBGL, graph, rorcid Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, lubridate, visNetwork, clipr, blastula, kableExtra, DiagrammeR, SummarizedExperiment License: MIT + file LICENSE MD5sum: 903b08b5f2f97f38a4a379dbdfe42150 NeedsCompilation: no Package: BiocSet Version: 1.12.1 Depends: R (>= 3.6), dplyr Imports: methods, tibble, utils, rlang, plyr, S4Vectors, BiocIO, AnnotationDbi, KEGGREST, ontologyIndex, tidyr Suggests: GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache, GO.db, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: c169d42e903c3a4fab052e1b0c2e2677 NeedsCompilation: no Package: BiocSingular Version: 1.14.0 Imports: BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat LinkingTo: Rcpp, beachmat Suggests: testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix License: GPL-3 MD5sum: 1c034e8eff7af96acb7060f203d698cd NeedsCompilation: yes Package: BiocSklearn Version: 1.20.1 Depends: R (>= 4.0), reticulate, methods, SummarizedExperiment Imports: basilisk Suggests: testthat, restfulSE, HDF5Array, BiocStyle, rmarkdown, knitr License: Artistic-2.0 MD5sum: c9a9ac896c43b8848a8bd06d946285c7 NeedsCompilation: no Package: BiocStyle Version: 2.26.0 Imports: bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils, yaml, BiocManager Suggests: BiocGenerics, RUnit, htmltools License: Artistic-2.0 MD5sum: 226b6f4cd70b8cbc70f3a0fb7c0c5039 NeedsCompilation: no Package: biocthis Version: 1.8.3 Imports: BiocManager, fs, glue, rlang, styler, usethis (>= 2.0.1) Suggests: BiocStyle, covr, devtools, knitr, pkgdown, RefManageR, rmarkdown, sessioninfo, testthat, utils License: Artistic-2.0 MD5sum: 9b2cc700b44fedafffb057b2805d2dd7 NeedsCompilation: no Package: BiocVersion Version: 3.16.0 Depends: R (>= 4.2.0) License: Artistic-2.0 MD5sum: 93a3b4f34283a2ed8a199e8d3912f037 NeedsCompilation: no Package: biocViews Version: 1.66.3 Depends: R (>= 3.6.0) Imports: Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools, utils, XML, RCurl, RUnit, BiocManager Suggests: BiocGenerics, knitr, commonmark, BiocStyle License: Artistic-2.0 MD5sum: e2f04a3df7eafbf3591f4e66e08a2296 NeedsCompilation: no Package: BiocWorkflowTools Version: 1.24.0 Depends: R (>= 3.4) Imports: BiocStyle, bookdown, git2r, httr, knitr, rmarkdown, rstudioapi, stringr, tools, utils, usethis License: MIT + file LICENSE MD5sum: ba2a60c07b35fce25fd357769bc19fda NeedsCompilation: no Package: biodb Version: 1.6.1 Depends: R (>= 4.1.0) Imports: BiocFileCache, R6, RCurl, RSQLite, Rcpp, XML, chk, jsonlite, lgr, lifecycle, methods, openssl, plyr, progress, rappdirs, stats, stringr, tools, withr, yaml LinkingTo: Rcpp, testthat Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2, git2r License: AGPL-3 MD5sum: e41073d023fab0a0c8e63a4d70deb20f NeedsCompilation: yes Package: biodbChebi Version: 1.4.0 Depends: R (>= 4.1) Imports: R6, biodb (>= 1.1.5) Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr License: AGPL-3 MD5sum: 0582144179a30a8feb6f001330e8ce80 NeedsCompilation: no Package: biodbExpasy Version: 1.2.0 Depends: R (>= 4.1) Imports: biodb (>= 1.3.1), R6, stringr, chk Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr License: AGPL-3 MD5sum: 29971b9c59da9baecd54e391f604e00c NeedsCompilation: no Package: biodbHmdb Version: 1.4.0 Depends: R (>= 4.1) Imports: R6, biodb (>= 1.3.2), Rcpp LinkingTo: Rcpp, testthat Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, lgr License: AGPL-3 MD5sum: 4c625a5697d02e9ec649e24c689175fa NeedsCompilation: yes Package: biodbKegg Version: 1.4.0 Depends: R (>= 4.1) Imports: R6, biodb (>= 1.4.2), chk, lifecycle Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, igraph, magick, lgr License: AGPL-3 MD5sum: bc718cc608d2b6192a74f74cef7c0757 NeedsCompilation: no Package: biodbLipidmaps Version: 1.4.1 Depends: R (>= 4.1) Imports: biodb (>= 1.3.2), lifecycle, R6 Suggests: BiocStyle, lgr, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr License: AGPL-3 MD5sum: 577c1bc6ee30f4e4731dad075d634848 NeedsCompilation: no Package: biodbMirbase Version: 1.2.2 Depends: R (>= 4.1) Imports: biodb (>= 1.3.1), R6, stringr, chk Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr License: AGPL-3 MD5sum: 6fe516069de42d9210072f74bc544619 NeedsCompilation: no Package: biodbNcbi Version: 1.2.0 Depends: R (>= 4.1) Imports: biodb (>= 1.3.2), R6, XML, chk Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr License: AGPL-3 MD5sum: 5bb846259fad18642609b9b73dd79bc0 NeedsCompilation: no Package: biodbNci Version: 1.2.0 Depends: R (>= 4.1) Imports: biodb (>= 1.3.1), R6, Rcpp, chk LinkingTo: Rcpp, testthat Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr License: AGPL-3 MD5sum: 3d48581ac261e785f8f20899598acffa NeedsCompilation: yes Package: biodbUniprot Version: 1.4.0 Depends: R (>= 4.1.0) Imports: R6, biodb (>= 1.4.2) Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr, covr License: AGPL-3 MD5sum: 343929da9c149f3bef983f1b4c1695c6 NeedsCompilation: no Package: bioDist Version: 1.70.0 Depends: R (>= 2.0), methods, Biobase,KernSmooth Suggests: locfit License: Artistic-2.0 MD5sum: ae3f92ffb044d8ddd7b79c40a25f91cb NeedsCompilation: no Package: biomaRt Version: 2.54.1 Depends: methods Imports: utils, XML (>= 3.99-0.7), AnnotationDbi, progress, stringr, httr, digest, BiocFileCache, rappdirs, xml2 Suggests: BiocStyle, knitr, mockery, rmarkdown, testthat, webmockr License: Artistic-2.0 MD5sum: 8838a78b5a25b7e5b74d26cf1b8a2403 NeedsCompilation: no Package: biomformat Version: 1.26.0 Depends: R (>= 3.2), methods Imports: plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5 Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) License: GPL-2 MD5sum: 021924c181e047394aace9efd7d498f8 NeedsCompilation: no Package: BioMM Version: 1.14.0 Depends: R (>= 3.6) Imports: stats, utils, grDevices, lattice, BiocParallel, glmnet, rms, precrec, nsprcomp, ranger, e1071, ggplot2, vioplot, CMplot, imager, topGO, xlsx Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 181ed1b7245517d5dc0a2c0ad75cd855 NeedsCompilation: no Package: BioMVCClass Version: 1.66.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz License: LGPL MD5sum: 63143097972f2eff40345d1bbb5550bf NeedsCompilation: no Package: biomvRCNS Version: 1.38.0 Depends: R (>= 3.5.0), IRanges, GenomicRanges, Gviz Imports: methods, mvtnorm Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 890c20df1dbdd0c83b8b6b833ba18871 NeedsCompilation: yes Package: BioNAR Version: 1.0.0 Depends: R (>= 3.5.0), igraph, poweRlaw, latex2exp, RSpectra, Rdpack Imports: stringr, synaptome.db, clusterCons, fgsea, grid, methods, scales, AnnotationDbi, dplyr, GO.db, org.Hs.eg.db, rSpectral, WGCNA, ggplot2, ggrepel Suggests: knitr, rmarkdown, igraphdata, testthat (>= 3.0.0), vdiffr, devtools, pander, plotly, randomcoloR License: Artistic-2.0 MD5sum: 59af065d7e33a18ae629d5b805b732f9 NeedsCompilation: no Package: BioNERO Version: 1.6.1 Depends: R (>= 4.1) Imports: WGCNA, dynamicTreeCut, matrixStats, sva, RColorBrewer, ComplexHeatmap, ggplot2, ggrepel, patchwork, reshape2, igraph, ggnetwork, intergraph, networkD3, ggnewscale, NetRep, stats, grDevices, graphics, utils, methods, BiocParallel, minet, GENIE3, SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2, covr License: GPL-3 MD5sum: 85e8ef0188240b7d9d0fe514d712b7c9 NeedsCompilation: no Package: BioNet Version: 1.58.0 Depends: R (>= 2.10.0), graph, RBGL Imports: igraph (>= 1.0.1), AnnotationDbi, Biobase Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML License: GPL (>= 2) MD5sum: 7537a515415a778836a02e20c93e2daf NeedsCompilation: no Package: BioNetStat Version: 1.18.0 Depends: R (>= 4.0), shiny, igraph, shinyBS, pathview, DT Imports: BiocParallel, RJSONIO, whisker, yaml, pheatmap, ggplot2, plyr, utils, stats, RColorBrewer, Hmisc, psych, knitr, rmarkdown, markdown License: GPL (>= 3) MD5sum: aedf149a8f3bcb6b4e51adc8e29a32da NeedsCompilation: no Package: BioQC Version: 1.26.0 Depends: R (>= 3.5.0), Biobase Imports: edgeR, Rcpp, methods, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db, ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer License: GPL (>= 3) + file LICENSE MD5sum: eddd368e698f022ce631789f40da4319 NeedsCompilation: yes Package: biosigner Version: 1.26.0 Imports: Biobase, methods, e1071, grDevices, graphics, MultiAssayExperiment, MultiDataSet, randomForest, ropls, stats, SummarizedExperiment, utils Suggests: BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, omicade4, rmarkdown, testthat License: CeCILL MD5sum: 60fa2538b344a969630de1198d161c01 NeedsCompilation: no Package: Biostrings Version: 2.66.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.31.2), XVector (>= 0.37.1), GenomeInfoDb Imports: methods, utils, grDevices, graphics, stats, crayon LinkingTo: S4Vectors, IRanges, XVector Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit Enhances: Rmpi License: Artistic-2.0 MD5sum: 0a8f1876901ffad59e00da7c74db5352 NeedsCompilation: yes Package: BioTIP Version: 1.12.0 Depends: R (>= 3.6) Imports: igraph, cluster, psych, stringr, GenomicRanges, MASS, scran Suggests: knitr, markdown, base, rmarkdown, ggplot2 License: GPL-2 MD5sum: debeb275ee85a57c16e5e569a1624960 NeedsCompilation: no Package: biotmle Version: 1.22.0 Depends: R (>= 4.0) Imports: stats, methods, dplyr, tibble, ggplot2, ggsci, superheat, assertthat, drtmle (>= 1.0.4), S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, limma Suggests: testthat, knitr, rmarkdown, BiocStyle, arm, earth, ranger, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) License: MIT + file LICENSE MD5sum: 434822e3db3e2e447e0e7c7d297799c7 NeedsCompilation: no Package: biovizBase Version: 1.46.0 Depends: R (>= 3.5.0), methods Imports: grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors (>= 0.23.19), IRanges (>= 1.99.28), GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21), SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>= 1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4), ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlang Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit License: Artistic-2.0 MD5sum: 2dc0a153a578a5dc82e5595a32e24089 NeedsCompilation: yes Package: BiRewire Version: 3.30.0 Depends: igraph, slam, Rtsne, Matrix Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 2ef7ae52e84cc2541bb70d3a75b44648 NeedsCompilation: yes Package: biscuiteer Version: 1.12.0 Depends: R (>= 4.1.0), biscuiteerData, bsseq Imports: readr, qualV, Matrix, impute, HDF5Array, S4Vectors, Rsamtools, data.table, Biobase, GenomicRanges, IRanges, BiocGenerics, VariantAnnotation, DelayedMatrixStats, SummarizedExperiment, GenomeInfoDb, Mus.musculus, Homo.sapiens, matrixStats, rtracklayer, QDNAseq, dmrseq, methods, utils, R.utils, gtools, BiocParallel Suggests: DSS, covr, knitr, rmarkdown, markdown, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10, BiocStyle License: GPL-3 MD5sum: d680ca31a47cf98af9fa5c3a7b7ec4eb NeedsCompilation: no Package: BiSeq Version: 1.38.0 Depends: R (>= 3.5.0), methods, S4Vectors, IRanges (>= 1.17.24), GenomicRanges, SummarizedExperiment (>= 0.2.0), Formula Imports: methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer, parallel, betareg, lokern, Formula, globaltest License: LGPL-3 MD5sum: e95fe02b16d38066b7ab706055aab081 NeedsCompilation: no Package: BitSeq Version: 1.41.0 Depends: Rsamtools (>= 1.99.3) Imports: S4Vectors, IRanges, methods, utils LinkingTo: Rhtslib (>= 1.15.5) Suggests: BiocStyle License: Artistic-2.0 + file LICENSE MD5sum: d461266598d29b16f5b6bddca83061ef NeedsCompilation: yes Package: blacksheepr Version: 1.12.0 Depends: R (>= 3.6) Imports: grid, stats, grDevices, utils, circlize, viridis, RColorBrewer, ComplexHeatmap, SummarizedExperiment, pasilla Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl License: MIT + file LICENSE MD5sum: 1e20177df9e32d3a2b62000faec31d9e NeedsCompilation: no Package: blima Version: 1.32.0 Depends: R(>= 3.3) Imports: beadarray(>= 2.0.0), Biobase(>= 2.0.0), Rcpp (>= 0.12.8), BiocGenerics, grDevices, stats, graphics LinkingTo: Rcpp Suggests: xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr License: GPL-3 MD5sum: 8ccffcd5590d1e04a45acabbd76f984f NeedsCompilation: yes Package: BLMA Version: 1.22.0 Depends: ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel, Biobase, metafor, methods Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: a5c4cb33e1247fdd14d6cce7f877df19 NeedsCompilation: no Package: BloodGen3Module Version: 1.6.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, ExperimentHub, methods, grid, graphics, stats, grDevices, circlize, testthat, ComplexHeatmap(>= 1.99.8), ggplot2, matrixStats, gtools, reshape2, preprocessCore, randomcoloR, V8, limma Suggests: RUnit, devtools, BiocGenerics, knitr, rmarkdown License: GPL-2 MD5sum: 5a0d4ae1698fdffe6f8d91ea2657baf1 NeedsCompilation: no Package: bluster Version: 1.8.0 Imports: stats, methods, utils, cluster, Matrix, Rcpp, igraph, S4Vectors, BiocParallel, BiocNeighbors LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut, scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans, kohonen, apcluster License: GPL-3 MD5sum: 4698411f72478c5b8a840281b72d9d9e NeedsCompilation: yes Package: bnbc Version: 1.20.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, GenomicRanges Imports: Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, GenomeInfoDb, S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: cdf39b35db170ecbe2be8035e3b93259 NeedsCompilation: yes Package: bnem Version: 1.6.0 Depends: R (>= 4.1) Imports: CellNOptR, matrixStats, snowfall, Rgraphviz, cluster, flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods, utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown Suggests: knitr, BiocGenerics License: GPL-3 MD5sum: 04804ab38025438dc9d0d64bbccdeddd NeedsCompilation: no Package: BOBaFIT Version: 1.2.0 Depends: R (>= 2.10) Imports: dplyr, NbClust, ggplot2, ggbio, grDevices, stats, tidyr, GenomicRanges, ggforce, stringr, plyranges, methods, utils, magrittr Suggests: rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0), utils, testthat License: GPL (>= 3) MD5sum: ea9ad057b5982223cd55b4c6dfc9508d NeedsCompilation: no Package: borealis Version: 1.2.2 Depends: R (>= 4.2.0), Biobase Imports: doParallel, snow, purrr, plyr, foreach, gamlss, gamlss.dist, bsseq, methods, DSS, R.utils, utils, stats, ggplot2, cowplot, dplyr, rlang, GenomicRanges Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, annotatr, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL-3 MD5sum: fb57b46a5208f7ef2a08f9902beacec7 NeedsCompilation: no Package: BPRMeth Version: 1.24.2 Depends: R (>= 3.5.0), GenomicRanges Imports: assertthat, methods, MASS, doParallel, parallel, e1071, earth, foreach, randomForest, stats, IRanges, S4Vectors, data.table, graphics, truncnorm, mvtnorm, Rcpp (>= 0.12.14), matrixcalc, magrittr, kernlab, ggplot2, cowplot, BiocStyle LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 1bd11df337708b265eecfb88ea34a0cc NeedsCompilation: yes Package: BRAIN Version: 1.44.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 MD5sum: 6cb636ac649543bb675f477ca5fdf7a8 NeedsCompilation: no Package: brainflowprobes Version: 1.12.0 Depends: R (>= 3.6.0) Imports: Biostrings (>= 2.52.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), bumphunter (>= 1.26.0), cowplot (>= 1.0.0), derfinder (>= 1.18.1), derfinderPlot (>= 1.18.1), GenomicRanges (>= 1.36.0), ggplot2 (>= 3.1.1), RColorBrewer (>= 1.1), utils, grDevices, GenomicState (>= 0.99.7) Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr License: Artistic-2.0 MD5sum: 581d38fac413337532381092c59afeee NeedsCompilation: no Package: BrainSABER Version: 1.8.0 Depends: R (>= 4.1.0), biomaRt, SummarizedExperiment Imports: data.table, lsa, methods, S4Vectors, utils, BiocFileCache, shiny Suggests: BiocStyle, ComplexHeatmap, fastcluster, heatmaply, knitr, plotly, rmarkdown License: Artistic-2.0 MD5sum: 5ef803604825ff12dc0dc612e5f987dc NeedsCompilation: no Package: branchpointer Version: 1.24.0 Depends: caret, R(>= 3.4) Imports: plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt, Biostrings, parallel, utils, stats, BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges, GenomeInfoDb, IRanges, S4Vectors, data.table Suggests: knitr, BiocStyle License: BSD_3_clause + file LICENSE MD5sum: fdbd1d83d96ade59470abd333637e3da NeedsCompilation: no Package: breakpointR Version: 1.16.0 Depends: R (>= 3.5), GenomicRanges, cowplot, breakpointRdata Imports: methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>= 1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2, BiocGenerics, gtools, doParallel, foreach Suggests: knitr, BiocStyle, testthat License: file LICENSE MD5sum: 34da220824ebf7a965d1ee67364bc1d3 NeedsCompilation: no Package: brendaDb Version: 1.12.0 Imports: dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel, crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, devtools License: MIT + file LICENSE MD5sum: ef642ac03af1060b439cbfd1619af06f NeedsCompilation: yes Package: BRGenomics Version: 1.10.0 Depends: R (>= 4.0), rtracklayer, GenomeInfoDb, S4Vectors Imports: GenomicRanges, parallel, IRanges, stats, Rsamtools, GenomicAlignments, DESeq2, SummarizedExperiment, utils, methods Suggests: BiocStyle, knitr, rmarkdown, testthat, apeglm, remotes, ggplot2, reshape2, Biostrings License: Artistic-2.0 MD5sum: 48f16fb86fff2cf4ede70737f51db599 NeedsCompilation: no Package: bridge Version: 1.62.0 Depends: R (>= 1.9.0), rama License: GPL (>= 2) MD5sum: 8827b980b1d8ef469f4b0988c39a31d0 NeedsCompilation: yes Package: BridgeDbR Version: 2.8.0 Depends: R (>= 3.3.0), rJava Imports: curl Suggests: BiocStyle, knitr, rmarkdown, testthat License: AGPL-3 MD5sum: 19105686f769045eff22e23256c6271c NeedsCompilation: no Package: BrowserViz Version: 2.20.0 Depends: R (>= 3.5.0), jsonlite (>= 1.5), httpuv(>= 1.5.0) Imports: methods, BiocGenerics Suggests: RUnit, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: aa90122bfd4b56e52a1a3a51b8c1838d NeedsCompilation: no Package: BSgenome Version: 1.66.3 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.25.6), GenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), rtracklayer (>= 1.39.7) Imports: methods, utils, stats, matrixStats, BiocGenerics, S4Vectors, IRanges, XVector (>= 0.29.3), GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, rtracklayer Suggests: BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit License: Artistic-2.0 MD5sum: 3db38e1f7e7fb0d685c4659e623b410f NeedsCompilation: no Package: bsseq Version: 1.34.0 Depends: R (>= 4.0), methods, BiocGenerics, GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5) Imports: IRanges (>= 2.23.9), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors (>= 0.27.12), R.utils (>= 2.0.0), DelayedMatrixStats (>= 1.5.2), permute, limma, DelayedArray (>= 0.15.16), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array (>= 1.19.11), rhdf5 LinkingTo: Rcpp, beachmat Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat (>= 1.5.2), BatchJobs License: Artistic-2.0 MD5sum: 295c85403b7f8c27ed534e157d89e19b NeedsCompilation: yes Package: BubbleTree Version: 2.28.0 Depends: R (>= 3.5), IRanges, GenomicRanges, plyr, dplyr, magrittr Imports: BiocGenerics (>= 0.31.6), BiocStyle, Biobase, ggplot2, WriteXLS, gtools, RColorBrewer, limma, grid, gtable, gridExtra, biovizBase, e1071, methods, grDevices, stats, utils Suggests: knitr, rmarkdown License: LGPL (>= 3) MD5sum: 5de859d09914c8875949f216ee088047 NeedsCompilation: no Package: BufferedMatrix Version: 1.62.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) MD5sum: e18e7b7edba2e994ba32c27260fcd69f NeedsCompilation: yes Package: BufferedMatrixMethods Version: 1.62.0 Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods LinkingTo: BufferedMatrix Suggests: affyio, affy License: GPL (>= 2) MD5sum: 1c53238a43259f250d21c7240b4657af NeedsCompilation: yes Package: bugsigdbr Version: 1.4.3 Depends: R (>= 4.1) Imports: BiocFileCache, methods, vroom, utils Suggests: BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 45530792fdde1e647d868d4b67aa2a09 NeedsCompilation: no Package: BUMHMM Version: 1.22.0 Depends: R (>= 3.5.0) Imports: devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges Suggests: testthat, knitr, BiocStyle License: GPL-3 MD5sum: ae2c6614e88d942903a1d660bee079de NeedsCompilation: no Package: bumphunter Version: 1.40.0 Depends: R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), GenomeInfoDb, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats Suggests: testthat, RUnit, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 11090040312a7467aea161f87c3e698f NeedsCompilation: no Package: BumpyMatrix Version: 1.6.0 Imports: utils, methods, Matrix, S4Vectors, IRanges Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 89450a903d6afc27773fe77ff4466628 NeedsCompilation: no Package: BUS Version: 1.54.0 Depends: R (>= 2.3.0), minet Imports: stats, infotheo License: GPL-3 MD5sum: 795ce8ceb3743ba0d277347c7fd0964b NeedsCompilation: yes Package: BUScorrect Version: 1.16.0 Depends: R (>= 3.5.0) Imports: gplots, methods, grDevices, stats, SummarizedExperiment Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 9a0174f9b7706b61138789c5916b9a7f NeedsCompilation: yes Package: BUSpaRse Version: 1.12.2 Depends: R (>= 3.6) Imports: AnnotationDbi, AnnotationFilter, biomaRt, BiocGenerics, Biostrings, BSgenome, dplyr, ensembldb, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, IRanges, magrittr, Matrix, methods, plyranges, Rcpp, S4Vectors, stats, stringr, tibble, tidyr, utils, zeallot LinkingTo: Rcpp, RcppArmadillo, RcppProgress, BH Suggests: knitr, rmarkdown, testthat, BiocStyle, TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: BSD_2_clause + file LICENSE MD5sum: e98132824f4f50aef7dcf42a3ca4a619 NeedsCompilation: yes Package: BUSseq Version: 1.4.2 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots, grDevices, methods, stats, utils Suggests: BiocStyle, knitr, BiocGenerics License: Artistic-2.0 MD5sum: 465e002323176343980266938e7a1ac2 NeedsCompilation: yes Package: CAEN Version: 1.6.0 Depends: R (>= 4.1) Imports: stats,PoiClaClu,SummarizedExperiment,methods Suggests: knitr,rmarkdown License: GPL-2 MD5sum: 4346618674e4f1318dc42bbd73f3b270 NeedsCompilation: no Package: CAFE Version: 1.34.0 Depends: R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio Imports: affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 62169e448f1215a7304f65f86a076695 NeedsCompilation: no Package: CAGEfightR Version: 1.18.0 Depends: R (>= 3.5), GenomicRanges (>= 1.30.1), rtracklayer (>= 1.38.2), SummarizedExperiment (>= 1.8.1) Imports: pryr(>= 0.1.3), assertthat(>= 0.2.0), methods(>= 3.6.3), Matrix(>= 1.2-12), BiocGenerics(>= 0.24.0), S4Vectors(>= 0.16.0), IRanges(>= 2.12.0), GenomeInfoDb(>= 1.14.0), GenomicFeatures(>= 1.29.11), GenomicAlignments(>= 1.22.1), BiocParallel(>= 1.12.0), GenomicFiles(>= 1.14.0), Gviz(>= 1.22.2), InteractionSet(>= 1.9.4), GenomicInteractions(>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-3 + file LICENSE MD5sum: 0506c9ea2f66d97185fd3f603830fa4f NeedsCompilation: no Package: cageminer Version: 1.4.0 Depends: R (>= 4.1) Imports: ggplot2, ggbio, ggtext, GenomeInfoDb, GenomicRanges, IRanges, reshape2, methods, BioNERO Suggests: testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo License: GPL-3 MD5sum: 316111044e2be074413c1c3504b7f560 NeedsCompilation: no Package: CAGEr Version: 2.4.0 Depends: methods, MultiAssayExperiment, R (>= 4.1.0) Imports: BiocGenerics, BiocParallel, BSgenome, data.table, DelayedArray, DelayedMatrixStats, formula.tools, GenomeInfoDb, GenomicAlignments, GenomicRanges (>= 1.37.16), ggplot2 (>= 2.2.0), gtools, IRanges (>= 2.18.0), KernSmooth, memoise, plyr, Rsamtools, reshape2, rtracklayer, S4Vectors (>= 0.27.5), som, stringdist, stringi, SummarizedExperiment, utils, vegan, VGAM Suggests: BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 68ec18ea718b95086d52c29ea6369b6a NeedsCompilation: no Package: calm Version: 1.12.0 Imports: mgcv, stats, graphics Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: d4fd62e2e7e4970b1f60bb0dcd92cb70 NeedsCompilation: no Package: CAMERA Version: 1.54.0 Depends: R (>= 3.5.0), methods, Biobase, xcms (>= 1.13.5) Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph Suggests: faahKO, RUnit, BiocGenerics Enhances: Rmpi, snow License: GPL (>= 2) MD5sum: 6406a3585bf0df9ba748dcba06cf20e5 NeedsCompilation: yes Package: canceR Version: 1.32.0 Depends: R (>= 4.1), tcltk Imports: GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart, survival, Biobase, phenoTest, circlize, plyr, graphics, stats, utils, grDevices, R.oo, R.methodsS3, httr Suggests: testthat (>= 3.1), knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 51791983ed57a2ed350a74b2abc42af3 NeedsCompilation: no Package: cancerclass Version: 1.42.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 MD5sum: cda38b5d70655976fec88534cfb4e03f NeedsCompilation: yes Package: CancerInSilico Version: 2.18.0 Depends: R (>= 3.4), Rcpp Imports: methods, utils, graphics, stats LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, BiocStyle, Rtsne, viridis, rgl, gplots License: GPL-2 MD5sum: 716dc250caa885da7b8b0783f0871e16 NeedsCompilation: yes Package: CancerSubtypes Version: 1.24.0 Depends: R (>= 4.0), sigclust, NMF Imports: cluster, impute, limma, ConsensusClusterPlus, grDevices, survival Suggests: BiocGenerics, knitr, RTCGA.mRNA, rmarkdown License: GPL (>= 2) MD5sum: 6408f7a2caaf66cf3fa980489f7ca579 NeedsCompilation: no Package: cardelino Version: 1.0.0 Depends: R (>= 4.2), stats Imports: combinat, GenomeInfoDb, GenomicRanges, ggplot2, ggtree, Matrix, matrixStats, methods, pheatmap, snpStats, S4Vectors, utils, VariantAnnotation, vcfR Suggests: BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat, VGAM Enhances: doMC License: GPL-3 MD5sum: 525534b70799dee1c832844736da4e2b NeedsCompilation: yes Package: Cardinal Version: 3.0.1 Depends: ProtGenerics, BiocGenerics, BiocParallel, EBImage, graphics, methods, S4Vectors (>= 0.27.3), stats Imports: Biobase, irlba, Matrix, matter, magrittr, mclust, nlme, parallel, signal, sp, stats4, utils, viridisLite Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 2c46e941821bd76a335c8183110843d2 NeedsCompilation: yes Package: CARNIVAL Version: 2.8.0 Depends: R (>= 4.0) Imports: readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson, rmarkdown Suggests: RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo License: GPL-3 MD5sum: 8a625a5d177683644276069e2ec83656 NeedsCompilation: no Package: casper Version: 2.32.0 Depends: R (>= 3.6.0), Biobase, IRanges, methods, GenomicRanges Imports: BiocGenerics (>= 0.31.6), coda, EBarrays, gaga, gtools, GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors (>= 0.9.25), sqldf, survival, VGAM Enhances: parallel License: GPL (>= 2) MD5sum: 7861bc853a3ed19eb4294b9df2e41c5a NeedsCompilation: yes Package: CATALYST Version: 1.22.0 Depends: R (>= 4.0), SingleCellExperiment Imports: circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot, data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel, ggridges, graphics, grDevices, grid, gridExtra, magrittr, Matrix, matrixStats, methods, nnls, purrr, RColorBrewer, reshape2, Rtsne, SummarizedExperiment, S4Vectors, scales, scater, stats Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot License: GPL (>= 2) MD5sum: fbb099454e99a5e73e65484e0cf569f2 NeedsCompilation: no Package: Category Version: 2.64.0 Depends: methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix Imports: utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db License: Artistic-2.0 MD5sum: 25661de98f2a1dd3a725ffc32fd87088 NeedsCompilation: no Package: categoryCompare Version: 1.42.0 Depends: R (>= 2.10), Biobase, BiocGenerics (>= 0.13.8), Imports: AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1), GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29), methods, grDevices, utils Suggests: knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown License: GPL-2 MD5sum: 13384458a320bba4f400bb5b7e46a0e4 NeedsCompilation: no Package: CausalR Version: 1.30.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: fbe15290f057338668875e6b43ceca18 NeedsCompilation: no Package: cbaf Version: 1.20.1 Depends: R (>= 4.1) Imports: BiocFileCache, RColorBrewer, cBioPortalData, genefilter, gplots, grDevices, stats, utils, openxlsx Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 115d84712602fa29faf41ee492e87a80 NeedsCompilation: no Package: CBEA Version: 1.2.0 Depends: R (>= 4.2.0) Imports: BiocParallel, BiocSet, dplyr, lmom, fitdistrplus, magrittr, methods, mixtools, Rcpp (>= 1.0.7), stats, SummarizedExperiment, tibble, TreeSummarizedExperiment, tidyr, glue, generics, rlang, goftest LinkingTo: Rcpp Suggests: phyloseq, BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyverse, roxygen2, mia, purrr License: MIT + file LICENSE MD5sum: 1f8ecb231aa28156f298d9876ef4568c NeedsCompilation: yes Package: cBioPortalData Version: 2.10.3 Depends: R (>= 4.2.0), AnVIL (>= 1.7.1), MultiAssayExperiment Imports: BiocFileCache (>= 1.5.3), digest, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment, RTCGAToolbox (>= 2.19.7), S4Vectors, SummarizedExperiment, stats, tibble, tidyr, TCGAutils (>= 1.9.4), utils Suggests: BiocStyle, knitr, survival, survminer, rmarkdown, testthat License: AGPL-3 MD5sum: 784d9c462a7386e9e290927827321a6e NeedsCompilation: no Package: cbpManager Version: 1.6.0 Depends: shiny, shinydashboard Imports: utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite, rapportools, basilisk, reticulate, shinyBS, shinycssloaders, rintrojs, markdown Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 0a95ceef8400c5025368ef64e6b32724 NeedsCompilation: no Package: ccfindR Version: 1.18.0 Depends: R (>= 3.6.0) Imports: stats, S4Vectors, utils, methods, Matrix, SummarizedExperiment, SingleCellExperiment, Rtsne, graphics, grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp, Rdpack (>= 0.7) LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 8ea675f3900bdcaf4dddf8be74a1695d NeedsCompilation: yes Package: ccImpute Version: 1.0.2 Imports: Rcpp, matrixStats, stats, SIMLR, BiocParallel LinkingTo: Rcpp, RcppEigen Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, SingleCellExperiment, mclust, testthat (>= 3.0.0) License: GPL-3 MD5sum: 1ac1abc19bb44bf0c2249b6a297363ef NeedsCompilation: yes Package: ccmap Version: 1.24.0 Imports: AnnotationDbi (>= 1.36.2), BiocManager (>= 1.30.4), ccdata (>= 1.1.2), doParallel (>= 1.0.10), data.table (>= 1.10.4), foreach (>= 1.4.3), parallel (>= 3.3.3), xgboost (>= 0.6.4), lsa (>= 0.73.1) Suggests: crossmeta, knitr, rmarkdown, testthat, lydata License: MIT + file LICENSE MD5sum: 2d0f89a7ecd5e5d211c68a1eb0ddeddb NeedsCompilation: no Package: CCPROMISE Version: 1.24.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: e5df52ec7c541dbe5abf101f600d5a40 NeedsCompilation: no Package: ccrepe Version: 1.34.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat License: MIT + file LICENSE MD5sum: c6b2ef4dd4e56156cde5af1694668736 NeedsCompilation: no Package: celaref Version: 1.16.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang, BiocGenerics, S4Vectors, readr, tibble, DelayedArray Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat License: GPL-3 MD5sum: def8841541fbb88e90e389155856ee82 NeedsCompilation: no Package: celda Version: 1.14.2 Depends: R (>= 4.0), SingleCellExperiment, Matrix Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, reshape2, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, scater (>= 1.14.4), scran, dbscan, DelayedArray, stringr, ComplexHeatmap, multipanelfigure, circlize LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData License: MIT + file LICENSE MD5sum: 2603abcb61b99eccd9d29dd81c68015b NeedsCompilation: yes Package: CellaRepertorium Version: 1.8.0 Depends: R (>= 4.0) Imports: dplyr, tibble, stringr, Biostrings, Rcpp, reshape2, methods, rlang (>= 0.3), purrr, Matrix, S4Vectors, BiocGenerics, tidyr, forcats, progress, stats, utils, generics, glue LinkingTo: Rcpp Suggests: testthat, readr, knitr, rmarkdown, ggplot2, BiocStyle, ggdendro, broom, lme4, RColorBrewer, SingleCellExperiment, scater, broom.mixed, cowplot, igraph, ggraph License: GPL-3 MD5sum: 48a4dd0487cead52230abf5ed7e7a0af NeedsCompilation: yes Package: CellBarcode Version: 1.4.0 Depends: R (>= 4.1.0) Imports: methods, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr, ggplot2, stringr, magrittr, ShortRead (>= 1.48.0), Biostrings (>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors, seqinr, zlibbioc LinkingTo: Rcpp, BH Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 1fd5df9967ebe140361b27ea20d1e84b NeedsCompilation: yes Package: cellbaseR Version: 1.22.0 Depends: R(>= 3.4) Imports: methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils, Rsamtools, BiocParallel, foreach, utils, parallel, doParallel Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation License: Apache License (== 2.0) MD5sum: c083374dafa795b5ebe6fb233f3d6ed3 NeedsCompilation: no Package: CellBench Version: 1.14.0 Depends: R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils Imports: BiocGenerics, BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, tidyselect, lubridate Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 License: GPL-3 MD5sum: aa09efb7df8ad188a110e6dea609c455 NeedsCompilation: no Package: cellHTS2 Version: 2.62.0 Depends: R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid Imports: GSEABase, Category, stats4, BiocGenerics Suggests: ggplot2 License: Artistic-2.0 MD5sum: b205b46809e7b5f298b169cd4f5b8820 NeedsCompilation: no Package: CelliD Version: 1.6.2 Depends: R (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment Imports: Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater, stringr, irlba, data.table, glue, pbapply, umap, Rtsne, reticulate, fastmatch, matrixStats, ggplot2, BiocParallel, SummarizedExperiment, fgsea LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel License: GPL-3 + file LICENSE MD5sum: d2064f0a093ee693877f42a65a3e4a6b NeedsCompilation: yes Package: cellity Version: 1.26.0 Depends: R (>= 3.3) Imports: AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid, mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats, topGO, utils Suggests: BiocStyle, caret, knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: 6b0693fd2235f9007ee4c51d0437ed1a NeedsCompilation: no Package: CellMapper Version: 1.24.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 MD5sum: 22bf22e2b604129c559f9b548377ef66 NeedsCompilation: no Package: cellmigRation Version: 1.6.0 Depends: R (>= 4.1), methods, foreach Imports: tiff, graphics, stats, utils, reshape2, parallel, doParallel, grDevices, matrixStats, FME, SpatialTools, sp, vioplot, FactoMineR, Hmisc Suggests: knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl License: GPL-2 MD5sum: 0e7346ecd57612d11e6d9bce52ff0faa NeedsCompilation: no Package: CellMixS Version: 1.14.0 Depends: kSamples, R (>= 4.0) Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne License: GPL (>= 2) MD5sum: 8d530f1dd51eed4e5f116cfb4f3eb069 NeedsCompilation: no Package: CellNOptR Version: 1.44.0 Depends: R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML, ggplot2, rmarkdown Imports: igraph, stringi, stringr Suggests: data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics, Enhances: doParallel, foreach License: GPL-3 MD5sum: e438afa72966a32111828601470f9750 NeedsCompilation: yes Package: cellscape Version: 1.22.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0), plyr (>= 1.8.3), dplyr (>= 0.4.3), gtools (>= 3.5.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 1701c0939c4550c1ef73fc2fff0e2d81 NeedsCompilation: no Package: CellScore Version: 1.18.0 Depends: R (>= 3.5.0) Imports: Biobase (>= 2.39.1), graphics (>= 3.5.0), grDevices (>= 3.5.0), gplots (>= 3.0.1), lsa (>= 0.73.1), methods (>= 3.5.0), RColorBrewer(>= 1.1-2), squash (>= 1.0.8), stats (>= 3.5.0), utils(>= 3.5.0) Suggests: hgu133plus2CellScore, knitr License: GPL-3 MD5sum: aaebfc5737cde4ceea6edce15ea93a66 NeedsCompilation: no Package: CellTrails Version: 1.16.0 Depends: R (>= 3.5), SingleCellExperiment Imports: BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats, ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv, reshape2, Rtsne, stats, splines, SummarizedExperiment, utils Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown License: Artistic-2.0 MD5sum: ed5caae7127f8a9705808b4aad121f41 NeedsCompilation: no Package: cellTree Version: 1.27.0 Depends: R (>= 3.3), topGO Imports: topicmodels, slam, maptpx, igraph, xtable, gplots Suggests: BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db, Biobase, tools License: Artistic-2.0 MD5sum: 09dd76ef8fac155feb230900554f963f NeedsCompilation: no Package: cellxgenedp Version: 1.2.2 Depends: dplyr Imports: httr, curl, jsonlite, utils, tools, shiny, DT, rjsoncons Suggests: zellkonverter, SingleCellExperiment, HDF5Array, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery License: Artistic-2.0 MD5sum: a527093bfc882291b356a95354dcb16e NeedsCompilation: no Package: CEMiTool Version: 1.22.0 Depends: R (>= 4.0) Imports: methods, scales, dplyr, data.table (>= 1.9.4), WGCNA, grid, ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler, fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools, pracma, intergraph, grDevices, utils, network, matrixStats, ggdendro, gridExtra, gtable, fastcluster Suggests: testthat, BiocManager License: GPL-3 MD5sum: 2fd357e544a8cd2072467d91315c1a0a NeedsCompilation: no Package: censcyt Version: 1.6.1 Depends: R (>= 4.0), diffcyt Imports: BiocParallel, broom.mixed, dirmult, dplyr, edgeR, fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp, purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment, survival, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 License: MIT + file LICENSE MD5sum: 4c30f4eba33c97242e721d741a9285b6 NeedsCompilation: no Package: Cepo Version: 1.4.0 Depends: GSEABase, R (>= 4.1) Imports: DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors, methods, SingleCellExperiment, SummarizedExperiment, ggplot2, rlang, grDevices, patchwork, reshape2, BiocParallel, stats, dplyr Suggests: knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap, patchwork License: MIT + file LICENSE MD5sum: b2a6d789154bb11b06542da41130f855 NeedsCompilation: no Package: ceRNAnetsim Version: 1.10.0 Depends: R (>= 4.0.0), dplyr, tidygraph Imports: furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, stats Suggests: knitr, png, rmarkdown, testthat, covr License: GPL (>= 3.0) MD5sum: 0ba92d9314ddb687b61cbf1dc4c6f865 NeedsCompilation: no Package: CeTF Version: 1.10.2 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, clusterProfiler, DESeq2, dplyr, GenomicTools.fileHandler, GGally, ggnetwork, ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3, stats, SummarizedExperiment, S4Vectors, utils, methods LinkingTo: Rcpp, RcppArmadillo Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat License: GPL-3 MD5sum: 28cedf0c4cd853a975391fc707b40af8 NeedsCompilation: yes Package: CexoR Version: 1.36.0 Depends: R (>= 4.2.0), S4Vectors, IRanges Imports: Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | GPL-2 + file LICENSE MD5sum: e7f2187bbbfee2532977ab3c274e3c08 NeedsCompilation: no Package: CFAssay Version: 1.32.0 Depends: R (>= 2.10.0) License: LGPL MD5sum: 36ca55c8314da07a31bd1b8a4fba1981 NeedsCompilation: no Package: cfDNAPro Version: 1.4.0 Depends: R (>= 4.1.0), magrittr (>= 1.5.0) Imports: tibble, GenomicAlignments, IRanges, plyranges, GenomeInfoDb, GenomicRanges, BiocGenerics, stats, utils, dplyr (>= 0.8.3), stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1), Rsamtools (>= 2.4.0), rlang (>= 0.4.0) Suggests: BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat License: GPL-3 MD5sum: fbf3fc44c1dc0538e3a0d36352e3b13e NeedsCompilation: no Package: CGEN Version: 3.34.3 Depends: R (>= 4.0), survival, mvtnorm Imports: stats, graphics, utils, grDevices Suggests: cluster License: GPL-2 + file LICENSE MD5sum: 2148ba0c8f18721bb7deb3ef2ace1a2c NeedsCompilation: yes Package: CGHbase Version: 1.58.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL MD5sum: ce342c83c38a08c2ef580abb3333a36e NeedsCompilation: no Package: CGHcall Version: 2.60.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall MD5sum: ab902489569708506d010a32d9100d0d NeedsCompilation: no Package: cghMCR Version: 1.56.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL MD5sum: 9c7845e115b75ebff33c9b64b94c2297 NeedsCompilation: no Package: CGHnormaliter Version: 1.52.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) MD5sum: ea6aef7b8e212d64a85aa6fbfff849f3 NeedsCompilation: no Package: CGHregions Version: 1.56.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase MD5sum: 5316ebaef92d8e2b990043fe7710a754 NeedsCompilation: no Package: ChAMP Version: 2.28.0 Depends: R (>= 3.3), minfi, ChAMPdata (>= 2.6.0),DMRcate, Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest, DT, RPMM Imports: prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b4.hg19, limma, DNAcopy, preprocessCore,impute, marray, wateRmelon, plyr,goseq,missMethyl,kpmt,ggplot2, GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly (>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat Suggests: knitr,rmarkdown License: GPL-3 MD5sum: 02dc474ce839ed542579b8f49ff2511c NeedsCompilation: no Package: ChemmineOB Version: 1.36.0 Depends: R (>= 2.15.1), methods Imports: BiocGenerics, zlibbioc, Rcpp (>= 0.11.0) LinkingTo: BH, Rcpp, zlibbioc Suggests: ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager, rmarkdown Enhances: ChemmineR (>= 2.13.0) License: file LICENSE MD5sum: 46652319b1500546c3c7c224b9f5e7ed NeedsCompilation: yes Package: ChemmineR Version: 3.50.0 Depends: R (>= 2.10.0), methods Imports: rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp (>= 0.11.0), ggplot2,grid,gridExtra, png,base64enc,DT,rsvg,jsonlite,stringi LinkingTo: Rcpp, BH Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png,rmarkdown, BiocManager,bibtex Enhances: ChemmineOB License: Artistic-2.0 MD5sum: e3d8cedf5f17fd8e90cf7924e2eec5e0 NeedsCompilation: yes Package: CHETAH Version: 1.14.0 Depends: R (>= 4.2), ggplot2, SingleCellExperiment Imports: shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr License: file LICENSE MD5sum: a52a859e01182cf8c33581b13ba93bae NeedsCompilation: no Package: ChIC Version: 1.18.0 Depends: spp, R (>= 3.6) Imports: ChIC.data (>= 1.11.1), caTools, methods, GenomicRanges, IRanges, parallel, progress, randomForest, caret, grDevices, stats, utils, graphics, S4Vectors, BiocGenerics, genomeIntervals, Rsamtools License: GPL-2 MD5sum: 70a3090cf6bb12d00eb12c6cfd5c6ac8 NeedsCompilation: no Package: Chicago Version: 1.26.0 Depends: R (>= 3.3.1), data.table Imports: matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub License: Artistic-2.0 MD5sum: b9c3508624df6f3cebbc449010119456 NeedsCompilation: no Package: chimeraviz Version: 1.24.0 Depends: Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, AnnotationFilter, data.table Imports: methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, checkmate, gtools, magick Suggests: testthat, roxygen2, devtools, knitr, lintr License: Artistic-2.0 MD5sum: 7f4150f23a890de4cd7b08c83320ce6b NeedsCompilation: no Package: ChIPanalyser Version: 1.20.0 Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb,RColorBrewer Suggests: BSgenome.Dmelanogaster.UCSC.dm6,knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 7fd61fb3752887826cd04c8ccb89fdf8 NeedsCompilation: no Package: ChIPComp Version: 1.28.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,rtracklayer,GenomeInfoDb,S4Vectors Imports: Rsamtools,limma,BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,BiocGenerics Suggests: BiocStyle,RUnit License: GPL MD5sum: ebe6fa661b216dc006bafd1e9e0bc6c4 NeedsCompilation: yes Package: chipenrich Version: 2.22.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, chipenrich.data, GenomeInfoDb, GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra, MASS, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer, S4Vectors (>= 0.23.10), stats, stringr, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat License: GPL-3 MD5sum: 3042e3493296572812e80941c35ed137 NeedsCompilation: no Package: ChIPexoQual Version: 1.22.0 Depends: R (>= 3.5.0), GenomicAlignments (>= 1.0.1) Imports: methods, utils, GenomeInfoDb, stats, BiocParallel, GenomicRanges (>= 1.14.4), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools (>= 1.16.1), IRanges (>= 1.6), S4Vectors (>= 0.8), biovizBase (>= 1.18), broom (>= 0.4), RColorBrewer (>= 1.1), dplyr (>= 0.5), scales (>= 0.4.0), viridis (>= 0.3), hexbin (>= 1.27), rmarkdown Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat License: GPL (>= 2) MD5sum: 7386edb04765f5dfdd4338b2a4f770ff NeedsCompilation: no Package: ChIPpeakAnno Version: 3.32.0 Depends: R (>= 3.5), methods, IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), S4Vectors (>= 0.17.25) Imports: AnnotationDbi, BiocGenerics (>= 0.1.0), Biostrings (>= 2.47.6), DBI, dplyr, ensembldb, GenomeInfoDb, GenomicAlignments, GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics, grid, InteractionSet, KEGGREST, matrixStats, multtest, regioneR, rtracklayer, stats, utils Suggests: AnnotationHub, BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, testthat, trackViewer, motifStack, OrganismDbi License: GPL (>= 2) MD5sum: e7776d3eea21385d4e3c394fc8aa3424 NeedsCompilation: no Package: ChIPQC Version: 1.34.1 Depends: R (>= 3.5.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19), BiocParallel Imports: BiocGenerics (>= 0.11.3), S4Vectors (>= 0.1.0), IRanges (>= 1.99.17), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), chipseq (>= 1.12.0), gtools, methods, reshape2, Nozzle.R1, Biobase, grDevices, stats, utils, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene Suggests: BiocStyle License: GPL (>= 3) MD5sum: ca1f27bd26ae5cd83fe4abf0ae5c9dd1 NeedsCompilation: no Package: ChIPseeker Version: 1.34.1 Depends: R (>= 3.5.0) Imports: AnnotationDbi, BiocGenerics, boot, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, graphics, grDevices, gtools, methods, plotrix, dplyr, parallel, magrittr, RColorBrewer, rtracklayer, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, tibble License: Artistic-2.0 MD5sum: 08517b750d902389822f02dcdd9ae93e NeedsCompilation: no Package: chipseq Version: 1.48.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), ShortRead Imports: methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges, ShortRead Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene License: Artistic-2.0 MD5sum: 12523fcdb2921dcd67ce0fd77d22ddf7 NeedsCompilation: yes Package: ChIPseqR Version: 1.52.0 Depends: R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25) Imports: Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14), graphics, grDevices, HilbertVis, ShortRead, stats, timsac, utils License: GPL (>= 2) MD5sum: 0f10d9a727359519b003c354ad5460c8 NeedsCompilation: yes Package: ChIPsim Version: 1.52.0 Depends: Biostrings (>= 2.29.2) Imports: IRanges, XVector, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) MD5sum: 73897564066708cf01ca43112dd3c895 NeedsCompilation: no Package: ChIPXpress Version: 1.42.0 Depends: R (>= 2.10), ChIPXpressData Imports: Biobase, GEOquery, frma, affy, bigmemory, biganalytics Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 92fafe405e063e4f03ae1569dd4384eb NeedsCompilation: no Package: chopsticks Version: 1.64.0 Imports: graphics, stats, utils, methods, survival Suggests: hexbin License: GPL-3 MD5sum: 6fec4040cd526a97457c35334689e4cb NeedsCompilation: yes Package: chromDraw Version: 2.28.0 Depends: R (>= 3.0.0) Imports: Rcpp (>= 0.11.1), GenomicRanges (>= 1.17.46) LinkingTo: Rcpp License: GPL-3 MD5sum: d14e634a9ce4023dc23fe1317bb6d201 NeedsCompilation: yes Package: ChromHeatMap Version: 1.52.0 Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0) Imports: Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer, GenomicRanges Suggests: ALL, hgu95av2.db License: Artistic-2.0 MD5sum: 9eee313b94d630cbbf3180996dd6927b NeedsCompilation: no Package: chromPlot Version: 1.26.0 Depends: stats, utils, graphics, grDevices, datasets, base, biomaRt, GenomicRanges, R (>= 3.1.0) Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 92c0f6ecc20d34fe9497eb91bbad444e NeedsCompilation: no Package: ChromSCape Version: 1.8.0 Depends: R (>= 4.1) Imports: shiny, colourpicker, shinyjs, rtracklayer, shinyFiles, shinyhelper, shinyWidgets, shinydashboardPlus, shinycssloaders, Matrix, plotly, shinydashboard, colorRamps, kableExtra, viridis, batchelor, BiocParallel, parallel, Rsamtools, ggplot2, ggrepel, gggenes, gridExtra, qualV, stringdist, stringr, fs, qs, DT, scran, scater, ConsensusClusterPlus, Rtsne, dplyr, tidyr, GenomicRanges, IRanges, irlba, rlist, umap, tibble, methods, jsonlite, edgeR, stats, graphics, grDevices, utils, S4Vectors, SingleCellExperiment, SummarizedExperiment, msigdbr, forcats, Rcpp, coop, matrixTests, DelayedArray LinkingTo: Rcpp Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr License: GPL-3 MD5sum: 9b9d43cc77922c6921a8a2c40c7b3d9d NeedsCompilation: yes Package: chromstaR Version: 1.24.0 Depends: R (>= 3.5.0), GenomicRanges, ggplot2, chromstaRData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, reshape2, Rsamtools, GenomicAlignments, bamsignals, mvtnorm Suggests: knitr, BiocStyle, testthat, biomaRt License: Artistic-2.0 MD5sum: 2c25efa82fab1bd33690a6577700f19b NeedsCompilation: yes Package: chromswitch Version: 1.20.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.26.4) Imports: cluster (>= 2.0.6), Biobase (>= 2.36.2), BiocParallel (>= 1.8.2), dplyr (>= 0.5.0), gplots(>= 3.0.1), graphics, grDevices, IRanges (>= 2.4.8), lazyeval (>= 0.2.0), matrixStats (>= 0.52), magrittr (>= 1.5), methods, NMF (>= 0.20.6), rtracklayer (>= 1.36.4), S4Vectors (>= 0.23.19), stats, tidyr (>= 0.6.3) Suggests: BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3), GenomeInfoDb (>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3), testthat License: MIT + file LICENSE MD5sum: 64fc31f3238fd1bcffb0d93068b7c6af NeedsCompilation: no Package: chromVAR Version: 1.20.2 Depends: R (>= 3.5.0) Imports: IRanges, GenomeInfoDb, GenomicRanges, ggplot2, nabor, BiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools, S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats, utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment, RColorBrewer, BSgenome LinkingTo: Rcpp, RcppArmadillo Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr License: MIT + file LICENSE MD5sum: ef863e0ecb0d442d151bb8d1a60e2c3b NeedsCompilation: yes Package: CHRONOS Version: 1.26.0 Depends: R (>= 3.5) Imports: XML, RCurl, RBGL, parallel, foreach, doParallel, openxlsx, igraph, circlize, graph, stats, utils, grDevices, graphics, methods, biomaRt, rJava Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL-2 MD5sum: ca4a9eaadbb4f1a5a574e173eec68e59 NeedsCompilation: no Package: cicero Version: 1.16.2 Depends: R (>= 3.5.0), monocle, Gviz (>= 1.22.3) Imports: assertthat (>= 0.2.0), Biobase (>= 2.37.2), BiocGenerics (>= 0.23.0), data.table (>= 1.10.4), dplyr (>= 0.7.4), FNN (>= 1.1), GenomicRanges (>= 1.30.3), ggplot2 (>= 2.2.1), glasso (>= 1.8), grDevices, igraph (>= 1.1.0), IRanges (>= 2.10.5), Matrix (>= 1.2-12), methods, parallel, plyr (>= 1.8.4), reshape2 (>= 1.4.3), S4Vectors (>= 0.14.7), stats, stringi, stringr (>= 1.2.0), tibble (>= 1.4.2), tidyr, VGAM (>= 1.0-5), utils Suggests: AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr License: MIT + file LICENSE MD5sum: b0b5995418250f045c280c3d6fd29a5b NeedsCompilation: no Package: CIMICE Version: 1.6.0 Imports: dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork, ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat, tidygraph, expm, Matrix Suggests: BiocStyle, knitr, rmarkdown, testthat, webshot License: Artistic-2.0 MD5sum: 067f4a89e8ceb27898e8926a71d931fb NeedsCompilation: no Package: CINdex Version: 1.26.0 Depends: R (>= 3.3), GenomicRanges Imports: bitops,gplots,grDevices,som, dplyr,gridExtra,png,stringr,S4Vectors, IRanges, GenomeInfoDb,graphics, stats, utils Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens, R.utils License: GPL (>= 2) MD5sum: b8104159cc449c9485b62a34d376505b NeedsCompilation: no Package: circRNAprofiler Version: 1.12.2 Depends: R(>= 4.2.0) Imports: dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2, edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb, universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, Biostrings, gwascat, BSgenome, Suggests: testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager, License: GPL-3 MD5sum: 1b8790b72126190820a8deab7d7134c1 NeedsCompilation: no Package: CircSeqAlignTk Version: 1.0.0 Depends: R (>= 4.2) Imports: stats, tools, utils, methods, S4Vectors, rlang, magrittr, dplyr, tidyr, ggplot2, BiocGenerics, Biostrings, IRanges, ShortRead, Rsamtools, Rbowtie2, Rhisat2 Suggests: knitr, rmarkdown, testthat, R.utils, BiocStyle License: MIT + file LICENSE MD5sum: b2aaeb513c902a58a5cc4e2d243042b2 NeedsCompilation: no Package: cisPath Version: 1.38.0 Depends: R (>= 2.10.0) Imports: methods, utils License: GPL (>= 3) MD5sum: 8f1af7ef0e763b6dab056251f14ef31a NeedsCompilation: yes Package: CiteFuse Version: 1.10.0 Depends: R (>= 4.0) Imports: SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>= 1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid, dbscan, propr, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph, scales, scran (>= 1.14.6), graphics, methods, stats, utils, reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5, rlang Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown License: GPL-3 MD5sum: 14f2a647d9266f4dfca6300610dadaf9 NeedsCompilation: no Package: ClassifyR Version: 3.2.7 Depends: R (>= 4.1.0), generics, methods, S4Vectors, MultiAssayExperiment, BiocParallel, survival Imports: grid, genefilter, utils, dplyr, tidyr, rlang, ranger Suggests: limma, edgeR, car, Rmixmod, ggplot2 (>= 3.0.0), gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, robustbase, glmnet, class, randomForestSRC, MatrixModels, xgboost License: GPL-3 MD5sum: 65d79214520ac63de7ab00347fc519aa NeedsCompilation: yes Package: cleanUpdTSeq Version: 1.36.0 Depends: R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods Imports: BSgenome, GenomicRanges, seqinr, e1071, Biostrings, GenomeInfoDb, IRanges, utils, stringr, stats, S4Vectors Suggests: BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0) License: GPL-2 MD5sum: 8c259d3d2eddcf20bc35f4324daf51d7 NeedsCompilation: no Package: cleaver Version: 1.36.0 Depends: R (>= 3.0.0), methods, Biostrings (>= 1.29.8) Imports: S4Vectors, IRanges Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.36.5) License: GPL (>= 3) MD5sum: 11a24b190615830308ce0a0c5701becd NeedsCompilation: no Package: clippda Version: 1.48.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>= 2) MD5sum: 08da96aea84b3ee08cf84f2736f5258f NeedsCompilation: no Package: clipper Version: 1.38.0 Depends: R (>= 2.15.0), Matrix, graph Imports: methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor, RBGL Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle Enhances: RCy3 License: AGPL-3 MD5sum: b70d35ef76965a6e10776313731e7a12 NeedsCompilation: no Package: cliProfiler Version: 1.4.0 Depends: S4Vectors, methods, R (>= 4.1) Imports: dplyr, rtracklayer, GenomicRanges, ggplot2, BSgenome, Biostrings, utils Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: 09046d98eb39f94dfd42272f5a4d77bc NeedsCompilation: no Package: cliqueMS Version: 1.12.2 Depends: R (>= 3.6.0) Imports: Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, qlcMatrix, matrixStats, methods LinkingTo: Rcpp, BH, RcppArmadillo Suggests: knitr, rmarkdown, testthat, CAMERA License: GPL (>= 2) MD5sum: 7ab9c65e054da01811bf9b9f72b96cd0 NeedsCompilation: yes Package: Clomial Version: 1.34.0 Depends: R (>= 2.10), matrixStats Imports: methods, permute License: GPL (>= 2) MD5sum: a01dc5636a3d650aeafe3eded92250bd NeedsCompilation: no Package: Clonality Version: 1.46.0 Depends: R (>= 2.12.2), DNAcopy Imports: grDevices, graphics, stats, utils Suggests: gdata License: GPL-3 MD5sum: a0299b04405e204ec17f61c10157fc35 NeedsCompilation: no Package: clst Version: 1.46.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 MD5sum: 31192f1730085270dc8910075bc5a9be NeedsCompilation: no Package: clstutils Version: 1.46.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit License: GPL-3 MD5sum: 55e243db171f8d4286ee6edf43181e80 NeedsCompilation: no Package: CluMSID Version: 1.14.0 Depends: R (>= 3.6) Imports: mzR, S4Vectors, dbscan, RColorBrewer, ape, network, GGally, ggplot2, plotly, methods, utils, stats, sna, grDevices, graphics, Biobase, gplots, MSnbase Suggests: knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms License: MIT + file LICENSE MD5sum: 95c1aa358fd631ef647ff53df0af018e NeedsCompilation: no Package: clustComp Version: 1.26.0 Depends: R (>= 3.3) Imports: sm, stats, graphics, grDevices Suggests: Biobase, colonCA, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 00e715730c8305ae8755a0ccf508f411 NeedsCompilation: no Package: clusterExperiment Version: 2.18.2 Depends: R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>= 1.15.4), BiocGenerics Imports: methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, howmany, locfdr, matrixStats, graphics, parallel, BiocSingular, kernlab, stringr, S4Vectors, grDevices, DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma, mbkmeans LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown License: Artistic-2.0 MD5sum: a40f13c9bf44c76916489853a12ab0b6 NeedsCompilation: yes Package: ClusterJudge Version: 1.20.0 Depends: R (>= 3.6), stats, utils, graphics, infotheo, lattice, latticeExtra, httr, jsonlite Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt License: Artistic-2.0 MD5sum: 55bf309c7ca917b967afab96e3490542 NeedsCompilation: no Package: clusterProfiler Version: 4.6.2 Depends: R (>= 3.5.0) Imports: AnnotationDbi, downloader, DOSE (>= 3.23.2), dplyr, enrichplot (>= 1.9.3), GO.db, GOSemSim, gson (>= 0.0.7), magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils Suggests: AnnotationHub, knitr, rmarkdown, org.Hs.eg.db, prettydoc, ReactomePA, testthat License: Artistic-2.0 MD5sum: cec2c019b8731fa6b37e74e0d73d7015 NeedsCompilation: no Package: clusterSeq Version: 1.22.0 Depends: R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats, utils Imports: BiocGenerics Suggests: BiocStyle License: GPL-3 MD5sum: 4ab3e551009171b8fc613cc27e76f0d0 NeedsCompilation: no Package: ClusterSignificance Version: 1.26.0 Depends: R (>= 3.3.0) Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr License: GPL-3 MD5sum: daa7c28296949b221850b3b867149723 NeedsCompilation: no Package: clusterStab Version: 1.70.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 MD5sum: 1724beb3fe1efe32ce25c25882d24d09 NeedsCompilation: no Package: clustifyr Version: 1.10.0 Depends: R (>= 3.5.0) Imports: cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, readr, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, matrixStats, S4Vectors, proxy, httr, utils Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, Seurat, gprofiler2, purrr License: MIT + file LICENSE MD5sum: 65ff873bbf6384c2b28f62b5545b05a4 NeedsCompilation: no Package: CMA Version: 1.56.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm License: GPL (>= 2) MD5sum: 2ec9d62ada714c1cdc0942d957cb8038 NeedsCompilation: no Package: cmapR Version: 1.10.0 Depends: R (>= 4.0) Imports: methods, rhdf5, data.table, flowCore, SummarizedExperiment, matrixStats Suggests: knitr, testthat, BiocStyle, rmarkdown License: file LICENSE MD5sum: 784186014a29cd30e2d0212b9509e1eb NeedsCompilation: no Package: cn.farms Version: 1.46.0 Depends: R (>= 3.0), Biobase, methods, ff, oligoClasses, snow Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 License: LGPL (>= 2.0) MD5sum: bd0750a42f29c050e9b24cdd62cfd235 NeedsCompilation: yes Package: cn.mops Version: 1.44.0 Depends: R (>= 3.5.0), methods, utils, stats, graphics, parallel, GenomicRanges Imports: BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb, S4Vectors, exomeCopy Suggests: DNAcopy License: LGPL (>= 2.0) MD5sum: b6bf66a32ff29f2b9e512500bd0386f0 NeedsCompilation: yes Package: CNAnorm Version: 1.44.3 Depends: R (>= 2.10.1), methods Imports: DNAcopy License: GPL-2 MD5sum: d4ff73bbd6cd0ac92ce65040c0636e13 NeedsCompilation: yes Package: CNEr Version: 1.34.0 Depends: R (>= 3.5.0) Imports: Biostrings (>= 2.33.4), DBI (>= 0.7), RSQLite (>= 0.11.4), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.23.16), rtracklayer (>= 1.25.5), XVector (>= 0.5.4), GenomicAlignments (>= 1.1.9), methods, S4Vectors (>= 0.13.13), IRanges (>= 2.5.27), readr (>= 0.2.2), BiocGenerics, tools, parallel, reshape2 (>= 1.4.1), ggplot2 (>= 2.1.0), poweRlaw (>= 0.60.3), annotate (>= 1.50.0), GO.db (>= 3.3.0), R.utils (>= 2.3.0), KEGGREST (>= 1.14.0) LinkingTo: S4Vectors, IRanges, XVector Suggests: Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3 License: GPL-2 | file LICENSE License_restricts_use: yes MD5sum: 81f050e673f6840a936db181b04b5566 NeedsCompilation: yes Package: CNORdt Version: 1.40.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 MD5sum: 3a1d5e1faf2bf1205f10a053c594ec19 NeedsCompilation: yes Package: CNORfeeder Version: 1.38.0 Depends: R (>= 3.6.0), CellNOptR (>= 1.4.0), graph Suggests: minet, catnet, Rgraphviz, RUnit, BiocGenerics, igraph Enhances: MEIGOR License: GPL-3 MD5sum: bd08b30eb1f73ae6e10a712c8e3ae940 NeedsCompilation: no Package: CNORfuzzy Version: 1.40.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 MD5sum: 8f53be92ad13d10c66b8297298221d0f NeedsCompilation: yes Package: CNORode Version: 1.40.0 Depends: CellNOptR, genalg, knitr Enhances: MEIGOR, doParallel, foreach License: GPL-2 MD5sum: d38ac5b9ea40fccdd4efb02afe3bd407 NeedsCompilation: yes Package: CNTools Version: 1.54.0 Depends: R (>= 2.10), methods, tools, stats, genefilter License: LGPL MD5sum: 4edaefb85eee163d531eba241e05d8df NeedsCompilation: yes Package: CNVfilteR Version: 1.12.2 Depends: R (>= 4.1) Imports: IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown License: Artistic-2.0 MD5sum: c7dbeb22092db917ce036fd90e805e30 NeedsCompilation: no Package: CNVgears Version: 1.6.0 Depends: R (>= 4.1), data.table Imports: ggplot2 Suggests: VariantAnnotation, DelayedArray, knitr, biomaRt, evobiR, rmarkdown, devtools, cowplot, usethis, scales, testthat, GenomicRanges, cn.mops, R.utils License: GPL-3 MD5sum: 3810d95060270e506c56d24dde5352f0 NeedsCompilation: no Package: cnvGSA Version: 1.42.0 Depends: brglm, doParallel, foreach, GenomicRanges, methods, splitstackshape Suggests: cnvGSAdata, org.Hs.eg.db License: LGPL MD5sum: 3a433de501c850e9023324d740ca2fce NeedsCompilation: no Package: CNViz Version: 1.6.0 Depends: R (>= 4.0), shiny (>= 1.5.0) Imports: dplyr, stats, utils, grDevices, plotly, karyoploteR, CopyNumberPlots, GenomicRanges, magrittr, DT, scales, graphics Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: 37a75170c81c1080176a3b1a14ac2fd1 NeedsCompilation: no Package: CNVMetrics Version: 1.2.0 Depends: R (>= 4.1) Imports: GenomicRanges, IRanges, S4Vectors, BiocParallel, methods, magrittr, stats, pheatmap, gridExtra, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 99eb635069617690dc0fba019f8d2211 NeedsCompilation: no Package: CNVPanelizer Version: 1.30.0 Depends: R (>= 3.2.0), GenomicRanges Imports: BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, exomeCopy, foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx Suggests: knitr, RUnit License: GPL-3 MD5sum: d5912fbc4bcc0f1d01d4f507750b9664 NeedsCompilation: no Package: CNVRanger Version: 1.14.0 Depends: GenomicRanges, RaggedExperiment Imports: BiocGenerics, BiocParallel, GDSArray, GenomeInfoDb, IRanges, S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR, gdsfmt, grDevices, lattice, limma, methods, plyr, qqman, rappdirs, reshape2, stats, utils Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, curatedTCGAData, ensembldb, grid, knitr, regioneR, rmarkdown License: Artistic-2.0 MD5sum: 989274fbcd20ed1f98306b589487aecb NeedsCompilation: no Package: CNVrd2 Version: 1.36.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 MD5sum: b111328cdda3706b344730d5e7532819 NeedsCompilation: no Package: CoCiteStats Version: 1.70.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL MD5sum: bc803ee260ba9fd3f4569d029bdc6545 NeedsCompilation: no Package: COCOA Version: 2.12.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices, simpleCache, fitdistrplus Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: bca4b890f49be10d6a5da3ffb942575f NeedsCompilation: no Package: codelink Version: 1.66.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 MD5sum: 20e9a7bbe95d5dc0b776cb942bb94827 NeedsCompilation: no Package: CODEX Version: 1.30.0 Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors Suggests: WES.1KG.WUGSC License: GPL-2 MD5sum: 790f5347cfb6832e984516548f4aa788 NeedsCompilation: no Package: coexnet Version: 1.19.1 Depends: R (>= 3.6) Imports: affy, siggenes, GEOquery, vsn, igraph, acde, Biobase, limma, graphics, stats, utils, STRINGdb, SummarizedExperiment, minet, rmarkdown Suggests: RUnit, BiocGenerics, knitr License: LGPL MD5sum: f9215da077a9b10c836431510d44be43 NeedsCompilation: no Package: CoGAPS Version: 3.18.0 Depends: R (>= 3.5.0) Imports: BiocParallel, cluster, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5 LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, BiocStyle License: BSD_3_clause + file LICENSE MD5sum: 05f7b1c2afa281c6c59e38513d4baafd NeedsCompilation: yes Package: cogena Version: 1.32.0 Depends: R (>= 3.6), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools Suggests: knitr, rmarkdown (>= 2.1) License: LGPL-3 MD5sum: 37198eecd973e419c7b2662e03e83864 NeedsCompilation: no Package: cogeqc Version: 1.2.1 Depends: R (>= 4.2.0) Imports: utils, graphics, stats, methods, reshape2, ggplot2, ggtree, patchwork, igraph, Biostrings Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr License: GPL-3 MD5sum: 3c18a968fdd923c8a1b254bfc43045ed NeedsCompilation: no Package: Cogito Version: 1.4.0 Depends: R (>= 4.1), GenomicRanges, jsonlite, GenomicFeatures, entropy Imports: BiocManager, rmarkdown, GenomeInfoDb, S4Vectors, AnnotationDbi, graphics, stats, utils, methods, magrittr, ggplot2, TxDb.Mmusculus.UCSC.mm9.knownGene Suggests: BiocStyle, knitr, markdown, testthat (>= 3.0.0) License: LGPL-3 MD5sum: 29b37b2f1a6717440ae3e1894a202705 NeedsCompilation: no Package: coGPS Version: 1.42.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 MD5sum: 920989190a041d2ba7837e1376949ed2 NeedsCompilation: no Package: COHCAP Version: 1.44.0 Depends: WriteXLS, COHCAPanno, RColorBrewer, gplots Imports: Rcpp, RcppArmadillo, BH LinkingTo: Rcpp, BH License: GPL-3 MD5sum: 9642e77797ebf65e2f773b4cb4e36974 NeedsCompilation: yes Package: cola Version: 2.4.0 Depends: R (>= 3.6.0) Imports: grDevices, graphics, grid, stats, utils, ComplexHeatmap (>= 2.5.4), matrixStats, GetoptLong, circlize (>= 0.4.7), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer, cluster, skmeans, png, mclust, crayon, methods, xml2, microbenchmark, httr, knitr, markdown, digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr, foreach, doParallel, irlba LinkingTo: Rcpp Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 License: MIT + file LICENSE MD5sum: 1e3ca280422b736d52ec750c077e08fb NeedsCompilation: yes Package: comapr Version: 1.2.0 Depends: R (>= 4.1.0) Imports: methods, ggplot2, reshape2, dplyr, gridExtra, plotly, circlize, rlang, GenomicRanges, IRanges, foreach, BiocParallel, GenomeInfoDb, scales, RColorBrewer, tidyr, S4Vectors, utils, Matrix, grid, stats, SummarizedExperiment, plyr, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod License: MIT + file LICENSE MD5sum: fd5a9990bdf9a7f13f841454f42d4b6c NeedsCompilation: no Package: combi Version: 1.10.0 Depends: R (>= 4.0), DBI Imports: ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix, BB, reshape2, alabama, cobs, Biobase, vegan, grDevices, graphics, methods, SummarizedExperiment Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: c9e6a26bf674cb1449d5e26bb8c92793 NeedsCompilation: no Package: coMET Version: 1.30.0 Depends: R (>= 4.1.0), grid, utils, biomaRt, Gviz, psych Imports: hash,grDevices, gridExtra, rtracklayer, IRanges, S4Vectors, GenomicRanges, stats, corrplot Suggests: BiocStyle, knitr, RUnit, BiocGenerics, showtext License: GPL (>= 2) MD5sum: 9fcd9137384d30c5e8c5a33a2cae6348 NeedsCompilation: no Package: coMethDMR Version: 1.2.0 Depends: R (>= 4.1) Imports: AnnotationHub, BiocParallel, bumphunter, ExperimentHub, GenomicRanges, IRanges, lmerTest, methods, stats, utils Suggests: BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: GPL-3 MD5sum: ed667bdf390dc369ce89186f710ce947 NeedsCompilation: no Package: compartmap Version: 1.16.0 Depends: R (>= 4.1.0), SummarizedExperiment, RaggedExperiment, BiocSingular, HDF5Array Imports: GenomicRanges, parallel, grid, ggplot2, reshape2, scales, DelayedArray, rtracklayer, DelayedMatrixStats, Matrix, RMTstat Suggests: covr, testthat, knitr, Rcpp, rmarkdown, markdown License: GPL-3 + file LICENSE MD5sum: 18e9415d9c03c94df8268c51f1561532 NeedsCompilation: no Package: COMPASS Version: 1.36.2 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach, coda LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress License: Artistic-2.0 MD5sum: 1dc79fa323fc773a82c16858ed23a96a NeedsCompilation: yes Package: compcodeR Version: 1.34.0 Depends: R (>= 4.0), sm Imports: tcltk, knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods, stats, utils, ape, phylolm, matrixStats, grDevices, graphics Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), baySeq (>= 2.2.0), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), rmarkdown, phytools, phangorn, testthat, ggtree, tidytree, statmod, covr Enhances: rpanel, DSS License: GPL (>= 2) MD5sum: 082c6a4af7c4a62a7ed52f1a494aaf19 NeedsCompilation: no Package: compEpiTools Version: 1.32.0 Depends: R (>= 3.5.0), methods, topGO, GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, GenomeInfoDb Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer License: GPL MD5sum: 9c9724694f3f5c54fe3b133a3381911f NeedsCompilation: no Package: ComplexHeatmap Version: 2.14.0 Depends: R (>= 3.5.0), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.14), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges, matrixStats, foreach, doParallel, codetools Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo License: MIT + file LICENSE MD5sum: 3f74a76dbc2cf5f97e7e8503cd30cbec NeedsCompilation: no Package: CompoundDb Version: 1.2.1 Depends: R (>= 4.1), methods, AnnotationFilter, S4Vectors Imports: BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics, xml2, IRanges, Spectra (>= 1.5.17), MsCoreUtils, MetaboCoreUtils Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf License: Artistic-2.0 MD5sum: 796b202426b8dfda5e0fece6810424ce NeedsCompilation: no Package: ComPrAn Version: 1.6.0 Imports: data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr, rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio, scales, shinydashboard, shinyjs, stats, tibble, grid Suggests: testthat (>= 2.1.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 9d1c8b4d8a68c42aced257aa76bd1d17 NeedsCompilation: no Package: conclus Version: 1.5.0 Depends: R (>= 4.1) Imports: org.Hs.eg.db, org.Mm.eg.db, dbscan, fpc, factoextra, Biobase, BiocFileCache, parallel, doParallel, foreach, SummarizedExperiment, biomaRt, AnnotationDbi, methods, dplyr, scran, scater, pheatmap, ggplot2, gridExtra, SingleCellExperiment, stats, utils, scales, grDevices, graphics, Rtsne, GEOquery, clusterProfiler, stringr, tools, rlang Suggests: knitr, rmarkdown, BiocStyle, S4Vectors, matrixStats, dynamicTreeCut, testthat License: GPL-3 MD5sum: c5ac0b9d2c24c49a7b8e59851273c7e2 NeedsCompilation: no Package: condiments Version: 1.6.0 Depends: R (>= 4.0) Imports: slingshot (>= 1.9), mgcv, RANN, stats, SingleCellExperiment, SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume (>= 0.9.1), methods, pbapply, matrixStats, BiocParallel, TrajectoryUtils, igraph, distinct Suggests: knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN License: MIT + file LICENSE MD5sum: e8ecd4e9abc639ed26daa7f68b5c9833 NeedsCompilation: no Package: CONFESS Version: 1.26.0 Depends: R (>= 3.3),grDevices,utils,stats,graphics Imports: methods,changepoint,cluster,contrast,data.table(>= 1.9.7),ecp,EBImage,flexmix,flowCore,flowClust,flowMeans,flowMerge,flowPeaks,foreach,ggplot2,grid,limma,MASS,moments,outliers,parallel,plotrix,raster,readbitmap,reshape2,SamSPECTRAL,waveslim,wavethresh,zoo Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata License: GPL-2 MD5sum: c833742de6232ed777c5dda94b15ad56 NeedsCompilation: no Package: consensus Version: 1.16.0 Depends: R (>= 3.5), RColorBrewer Imports: matrixStats, gplots, grDevices, methods, graphics, stats, utils Suggests: knitr, RUnit, rmarkdown, BiocGenerics License: BSD_3_clause + file LICENSE MD5sum: ed1069b27edb3379a74014375d8ab5c9 NeedsCompilation: no Package: ConsensusClusterPlus Version: 1.62.0 Imports: Biobase, ALL, graphics, stats, utils, cluster License: GPL-2 MD5sum: 37640754a7b0ce9b833b696163bf896f NeedsCompilation: no Package: consensusDE Version: 1.16.0 Depends: R (>= 3.5), BiocGenerics Imports: airway, AnnotationDbi, BiocParallel, Biobase, Biostrings, data.table, dendextend, DESeq2 (>= 1.20.0), EDASeq, ensembldb, edgeR, EnsDb.Hsapiens.v86, GenomicAlignments, GenomicFeatures, limma, org.Hs.eg.db, pcaMethods, RColorBrewer, Rsamtools, RUVSeq, S4Vectors, stats, SummarizedExperiment, TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: d5a3690f399ddd87c4ab8cafa5c2d5f8 NeedsCompilation: no Package: consensusOV Version: 1.20.0 Depends: R (>= 3.6) Imports: Biobase, GSVA, gdata, genefu, limma, matrixStats, randomForest, stats, utils, methods Suggests: BiocStyle, ggplot2, knitr, rmarkdown License: Artistic-2.0 MD5sum: cb6b145d2525dece177342dab97e584a NeedsCompilation: no Package: consensusSeekeR Version: 1.26.0 Depends: R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, BiocParallel Imports: GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 7e9954a729837824df09ab6d15ba3162 NeedsCompilation: no Package: consICA Version: 1.0.0 Depends: R (>= 4.2.0) Imports: fastICA (>= 1.2.1), sm, org.Hs.eg.db, GO.db, stats, SummarizedExperiment, BiocParallel, graph, methods, pheatmap, survival, topGO, graphics, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: MIT + file LICENSE MD5sum: a68f9698514cac4d6f1a152bcfb3f897 NeedsCompilation: no Package: CONSTANd Version: 1.6.0 Depends: R (>= 4.1) Suggests: BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma License: file LICENSE MD5sum: d16d1b1eccd7c3359db20df3dc1e8cf5 NeedsCompilation: no Package: contiBAIT Version: 1.26.0 Depends: R (>= 3.5.0), BH (>= 1.51.0.3), Rsamtools (>= 1.21) Imports: data.table, grDevices, clue, cluster, gplots, BiocGenerics (>= 0.31.6), S4Vectors, IRanges, GenomicRanges, Rcpp, TSP, GenomicFiles, gtools, rtracklayer, BiocParallel, DNAcopy, colorspace, reshape2, ggplot2, methods, exomeCopy, GenomicAlignments, diagram LinkingTo: Rcpp, BH Suggests: BiocStyle License: BSD_2_clause + file LICENSE MD5sum: 114e2fefb0e81e5d9e88c27efb6eb0ff NeedsCompilation: yes Package: conumee Version: 1.32.0 Depends: R (>= 3.5.0), minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest Imports: methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges, GenomeInfoDb Suggests: BiocStyle, knitr, rmarkdown, minfiData, RCurl License: GPL (>= 2) MD5sum: a7b423e994e2b0438500c0a6d0a4b487 NeedsCompilation: no Package: convert Version: 1.74.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL MD5sum: 81ae2cee0a80dda4f5cdf080b9f13b81 NeedsCompilation: no Package: copa Version: 1.66.0 Depends: Biobase, methods Suggests: colonCA License: Artistic-2.0 MD5sum: 83b2f1f4b5dacf38c4ed90598acfaa4c NeedsCompilation: yes Package: copynumber Version: 1.38.0 Depends: R (>= 2.10), BiocGenerics Imports: S4Vectors, IRanges, GenomicRanges License: Artistic-2.0 MD5sum: 1b7a578d6f0ae8a5c59c65e7d65ea0cb NeedsCompilation: no Package: CopyNumberPlots Version: 1.14.0 Depends: R (>= 3.6), karyoploteR Imports: regioneR, IRanges, Rsamtools, SummarizedExperiment, VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges, cn.mops, rhdf5, utils Suggests: BiocStyle, knitr, rmarkdown, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat License: Artistic-2.0 MD5sum: 580fd73da28dba64e9253aae671b78bb NeedsCompilation: no Package: CopywriteR Version: 2.29.0 Depends: R(>= 3.2), BiocParallel Imports: matrixStats, gtools, data.table, S4Vectors, chipseq, IRanges, Rsamtools, DNAcopy, GenomicAlignments, GenomicRanges, CopyhelpeR, GenomeInfoDb, futile.logger Suggests: BiocStyle, SCLCBam, snow License: GPL-2 MD5sum: fe013866bd29c06974f5e7ac3b3beae3 NeedsCompilation: no Package: coRdon Version: 1.16.0 Depends: R (>= 3.5) Imports: methods, stats, utils, Biostrings, Biobase, dplyr, stringr, purrr, ggplot2, data.table Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: cf6eef6d839305dc61687acb436fe61e NeedsCompilation: no Package: CoRegNet Version: 1.36.0 Depends: R (>= 2.14), igraph, shiny, arules, methods Suggests: RColorBrewer, gplots, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 0a37dda69c3814d6b53db91d90eab7e9 NeedsCompilation: yes Package: CoreGx Version: 2.2.0 Depends: R (>= 4.1), BiocGenerics, SummarizedExperiment Imports: Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics, piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods, stats, utils, graphics, grDevices, lsa, data.table, crayon, glue, rlang, bench Suggests: pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat License: GPL (>= 3) MD5sum: ce8eedafc085e5999f8e2471dfe9021f NeedsCompilation: no Package: Cormotif Version: 1.44.0 Depends: R (>= 2.12.0), affy, limma Imports: affy, graphics, grDevices License: GPL-2 MD5sum: f1c775ad7d0d21b09cf313cd4a69aeb0 NeedsCompilation: no Package: corral Version: 1.8.0 Imports: ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix, methods, MultiAssayExperiment, pals, reshape2, SingleCellExperiment, SummarizedExperiment, transport Suggests: ade4, BiocStyle, CellBench, DuoClustering2018, knitr, rmarkdown, scater, testthat License: GPL-2 MD5sum: ba1f3542ef1b8d0440a93425d1c6fb12 NeedsCompilation: no Package: CORREP Version: 1.64.0 Imports: e1071, stats Suggests: cluster, MASS License: GPL (>= 2) MD5sum: 35b2852aff08faa07ffdfc251f57f1bd NeedsCompilation: no Package: coseq Version: 1.22.0 Depends: R (>= 4.0.0), SummarizedExperiment, S4Vectors Imports: edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2, scales, HTSFilter, corrplot, HTSCluster, grDevices, graphics, stats, methods, compositions, mvtnorm Suggests: Biobase, knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 981e3921b8c8b0ef7464a76b08260aea NeedsCompilation: no Package: cosmiq Version: 1.32.0 Depends: R (>= 3.6), Rcpp Imports: pracma, xcms, MassSpecWavelet, faahKO Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: a125419fb5edd79a3cb29f247a5b8f82 NeedsCompilation: yes Package: cosmosR Version: 1.6.0 Depends: R (>= 4.1) Imports: CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr, rlang, stringr, utils, visNetwork Suggests: testthat, knitr, rmarkdown, piano, ggplot2 License: GPL-3 MD5sum: 89beb9a3a8e0d0bd9c7bf6866e3854e1 NeedsCompilation: no Package: COSNet Version: 1.32.0 Suggests: bionetdata, PerfMeas, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 02935b7d1b0af43a1d320f62abda00af NeedsCompilation: yes Package: COTAN Version: 1.2.0 Depends: R (>= 4.1) Imports: dplyr, methods, grDevices, Matrix, ggplot2, ggrepel, stats, parallel, tibble, tidyr, irlba, ComplexHeatmap, circlize, grid, scales, utils, rlang, Rfast Suggests: testthat (>= 3.0.0), spelling, knitr, data.table, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, factoextra, Rtsne, plotly, dendextend, BiocStyle, cowplot License: GPL-3 MD5sum: ee4bcf7168bf9c2660df2a703c5417bf NeedsCompilation: no Package: countsimQC Version: 1.16.1 Depends: R (>= 3.5) Imports: rmarkdown (>= 2.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr, ggplot2, grDevices, tools, SummarizedExperiment, genefilter, DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods, ragg Suggests: knitr, testthat License: GPL (>= 2) MD5sum: d87b41edc8ee829fb2afb773cdbac8e4 NeedsCompilation: no Package: covEB Version: 1.24.0 Depends: R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats, LaplacesDemon, Matrix Suggests: curatedBladderData License: GPL-3 MD5sum: 47716944fd4baeb049a3a39989a78d91 NeedsCompilation: no Package: CoverageView Version: 1.36.0 Depends: R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer Imports: S4Vectors (>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges, GenomicAlignments, parallel, tools License: Artistic-2.0 MD5sum: 50f935d5a62ee30ca9f66d7e932a236d NeedsCompilation: no Package: covRNA Version: 1.24.0 Depends: ade4, Biobase Imports: parallel, genefilter, grDevices, stats, graphics Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 9c4597b6990b7979f62c0f8f165a1db9 NeedsCompilation: no Package: cpvSNP Version: 1.30.0 Depends: R (>= 3.5.0), GenomicFeatures, GSEABase (>= 1.24.0) Imports: methods, corpcor, BiocParallel, ggplot2, plyr Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: 65344f26be01a2ca4c35bf91e70bc02b NeedsCompilation: no Package: cqn Version: 1.44.0 Depends: R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore, splines, quantreg Imports: splines Suggests: scales, edgeR License: Artistic-2.0 MD5sum: a7756a2cb20d4ff524581a71d9cbd2dd NeedsCompilation: no Package: CRImage Version: 1.46.0 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach, sgeostat License: Artistic-2.0 MD5sum: ac2eeb59822675b03e90b3bd23b98ad8 NeedsCompilation: no Package: crisprBase Version: 1.2.0 Depends: utils, methods, R (>= 4.1) Imports: BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges, S4Vectors, stringr Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 25b007b883909ea8f067909054993e38 NeedsCompilation: no Package: crisprBowtie Version: 1.2.0 Depends: methods Imports: BiocGenerics, Biostrings, BSgenome, crisprBase (>= 0.99.15), GenomeInfoDb, GenomicRanges, IRanges, Rbowtie, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: f625ba1a4390ea7dfb3086653d558f44 NeedsCompilation: no Package: crisprBwa Version: 1.2.0 Depends: methods Imports: BiocGenerics, BSgenome, crisprBase (>= 0.99.15), GenomeInfoDb, Rbwa, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE OS_type: unix MD5sum: 6cd9bd5cf9975bd37ef5bfae438ab91b NeedsCompilation: no Package: crisprDesign Version: 1.0.0 Depends: R (>= 4.2.0), crisprBase (>= 1.1.3) Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, crisprBowtie (>= 0.99.8), crisprScore (>= 1.1.6), GenomeInfoDb, GenomicFeatures, GenomicRanges (>= 1.38.0), IRanges, Matrix, MatrixGenerics, methods, rtracklayer, S4Vectors, stats, utils, VariantAnnotation Suggests: biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat License: MIT + file LICENSE MD5sum: 21ee312a0ac3825e1eca0d386f32c991 NeedsCompilation: no Package: crisprScore Version: 1.2.0 Depends: R (>= 4.1), crisprScoreData (>= 1.1.3) Imports: basilisk (>= 1.9.2), basilisk.utils (>= 1.9.1), BiocGenerics, Biostrings, IRanges, methods, randomForest, reticulate, stringr, utils, XVector Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: e0f272b62ca271ee8f51193beb2b057f NeedsCompilation: no Package: CRISPRseek Version: 1.38.0 Depends: R (>= 3.5.0), BiocGenerics, Biostrings Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges, BSgenome, hash, methods,reticulate,rhdf5,XVector, DelayedArray, GenomeInfoDb, GenomicRanges, dplyr, keras, mltools Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice, MASS, tensorflow, testthat License: GPL (>= 2) MD5sum: 7861d3f38219224811149b0d2016f3ad NeedsCompilation: no Package: crisprseekplus Version: 1.24.0 Depends: R (>= 3.3.0), shiny, shinyjs, CRISPRseek Imports: DT, utils, GUIDEseq, GenomicRanges, GenomicFeatures, BiocManager, BSgenome, AnnotationDbi, hash Suggests: testthat, rmarkdown, knitr, R.rsp License: GPL-3 + file LICENSE MD5sum: 5bf5e38c23e46788f2f63f404e24631b NeedsCompilation: no Package: CrispRVariants Version: 1.26.0 Depends: R (>= 3.5), ggplot2 (>= 2.2.0) Imports: AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>= 0.9.38), utils Suggests: BiocStyle, gdata, GenomicFeatures, knitr, rmarkdown, rtracklayer, sangerseqR, testthat, VariantAnnotation License: GPL-2 MD5sum: 8935a490224fa7a8832884804c1429db NeedsCompilation: no Package: crisprVerse Version: 1.0.0 Depends: R (>= 4.2.0) Imports: BiocManager, cli, crisprBase, crisprBowtie, crisprScore, crisprDesign, crisprViz, rlang, tools, utils Suggests: BiocStyle, knitr, testthat License: MIT + file LICENSE MD5sum: ae05e9e2ea7b5e4ba7a0b8a625ff9ebc NeedsCompilation: no Package: crisprViz Version: 1.0.0 Depends: R (>= 4.2.0), crisprBase (>= 0.99.15), crisprDesign (>= 0.99.77) Imports: BiocGenerics, Biostrings, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, grDevices, Gviz, IRanges, methods, S4Vectors Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, rtracklayer, testthat, utils License: MIT + file LICENSE MD5sum: d1413128c05af09b0b5651cfbf63bfc2 NeedsCompilation: no Package: crlmm Version: 1.56.0 Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= 1.17.7) Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>= 1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats, VGAM, parallel, graphics, limma, beanplot LinkingTo: preprocessCore (>= 1.17.7) Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit License: Artistic-2.0 MD5sum: a0290f707a9629b463eb4e72e2432891 NeedsCompilation: yes Package: crossmeta Version: 1.24.0 Depends: R (>= 4.0) Imports: affy (>= 1.52.0), affxparser (>= 1.46.0), AnnotationDbi (>= 1.36.2), Biobase (>= 2.34.0), BiocGenerics (>= 0.20.0), BiocManager (>= 1.30.4), DT (>= 0.2), DBI (>= 1.0.0), data.table (>= 1.10.4), edgeR, fdrtool (>= 1.2.15), GEOquery (>= 2.40.0), limma (>= 3.30.13), matrixStats (>= 0.51.0), metaMA (>= 3.1.2), miniUI (>= 0.1.1), methods, oligo (>= 1.38.0), reader(>= 1.0.6), RCurl (>= 1.95.4.11), RSQLite (>= 2.1.1), stringr (>= 1.2.0), sva (>= 3.22.0), shiny (>= 1.0.0), shinyjs (>= 2.0.0), shinyBS (>= 0.61), shinyWidgets (>= 0.5.3), shinypanel (>= 0.1.0), tibble, XML (>= 3.98.1.17), readxl (>= 1.3.1) Suggests: knitr, rmarkdown, lydata, org.Hs.eg.db, testthat License: MIT + file LICENSE MD5sum: c1f51276768ffd0643fda7879d1f6951 NeedsCompilation: no Package: CSAR Version: 1.50.0 Depends: R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 MD5sum: 8787c20f9005babb77c30ad68bca7366 NeedsCompilation: yes Package: csaw Version: 1.32.0 Depends: R (>= 3.5.0), GenomicRanges, SummarizedExperiment Imports: Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, metapod, utils LinkingTo: Rhtslib, zlibbioc, Rcpp Suggests: AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager License: GPL-3 MD5sum: 53bd00812612d98207c271671a86df28 NeedsCompilation: yes Package: csdR Version: 1.4.0 Depends: R (>= 4.1.0) Imports: WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp LinkingTo: Rcpp Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr License: GPL-3 MD5sum: 1d5d1e1e079747f9abd387eea3269c37 NeedsCompilation: yes Package: CSSP Version: 1.36.0 Imports: methods, splines, stats, utils Suggests: testthat License: GPL-2 MD5sum: 95dc8c5365a6fdccc307e6c6439f2c01 NeedsCompilation: yes Package: CSSQ Version: 1.10.0 Depends: SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, rtracklayer Imports: GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, markdown License: Artistic-2.0 MD5sum: 53db5989eb6ac0ffb3ff83af4bc62ef8 NeedsCompilation: no Package: ctc Version: 1.72.0 Depends: amap License: GPL-2 MD5sum: c0c8b37aef2d4ac25d88f2f85fad7bd1 NeedsCompilation: no Package: CTDquerier Version: 2.6.0 Depends: R (>= 4.1) Imports: RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils, grid, gridExtra, methods, stats, BiocFileCache Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: ba577b0b47524fe9337fd4e3efd67553 NeedsCompilation: no Package: cTRAP Version: 1.16.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, binr, cowplot, data.table, dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics, highcharter, htmltools, httr, limma, methods, parallel, pbapply, purrr, qs, R.utils, readxl, reshape2, rhdf5, rlang, scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble, tools, utils Suggests: testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes License: MIT + file LICENSE MD5sum: 8d3559b912d8367ccc625bd9a0e91fa4 NeedsCompilation: no Package: ctsGE Version: 1.24.0 Depends: R (>= 3.2) Imports: ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat License: GPL-2 MD5sum: 2cdec15fa80267e18281aee7f4313698 NeedsCompilation: no Package: CTSV Version: 1.0.0 Depends: R (>= 4.2), Imports: stats, pscl, qvalue, BiocParallel, methods, knitr, SpatialExperiment, SummarizedExperiment Suggests: testthat, BiocStyle License: GPL-3 MD5sum: 344992bc0638c5c06fd46ebe6ecf77ac NeedsCompilation: yes Package: cummeRbund Version: 2.40.0 Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz Imports: methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson License: Artistic-2.0 MD5sum: a1342d9f6f0b921c29f50b5e7260ede7 NeedsCompilation: no Package: customCMPdb Version: 1.8.0 Depends: R (>= 4.0) Imports: AnnotationHub, RSQLite, XML, utils, ChemmineR, methods, stats, rappdirs, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: 080cd0d0cfdb6834b772f31f3dcf95bd NeedsCompilation: no Package: customProDB Version: 1.38.0 Depends: R (>= 3.5.0), IRanges, AnnotationDbi, biomaRt (>= 2.17.1) Imports: S4Vectors (>= 0.9.25), DBI, GenomeInfoDb, GenomicRanges, Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>= 2.26.3), GenomicFeatures (>= 1.32.0), stringr, RCurl, plyr, VariantAnnotation (>= 1.13.44), rtracklayer, RSQLite, AhoCorasickTrie, methods Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 63307a7c99f1fffb9a156a761663580a NeedsCompilation: no Package: cyanoFilter Version: 1.6.0 Depends: R(>= 4.1.0) Imports: Biobase, flowCore, flowDensity, flowClust, cytometree, ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats, utils Suggests: magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr License: MIT + file LICENSE MD5sum: eeb7d85f0c12e350bcd2c0040958c440 NeedsCompilation: no Package: cycle Version: 1.52.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 MD5sum: 2fd4015a2a012a16a55ef20c9290265b NeedsCompilation: no Package: cydar Version: 1.22.0 Depends: SingleCellExperiment Imports: viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment, flowCore, Biobase, Rcpp, BiocNeighbors LinkingTo: Rcpp Suggests: ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet, BiocStyle, flowStats License: GPL-3 MD5sum: c78c0371107cab0d00786b9dec03d3c2 NeedsCompilation: yes Package: CytoDx Version: 1.18.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 95d2685deac2619ca30eb1713546a419 NeedsCompilation: no Package: CyTOFpower Version: 1.4.0 Depends: R (>= 4.1) Imports: CytoGLMM, diffcyt, DT, dplyr, ggplot2, magrittr, methods, rlang, stats, shiny, shinyFeedback, shinyjs, shinyMatrix, SummarizedExperiment, tibble, tidyr Suggests: testthat (>= 3.0.0), BiocStyle, knitr License: LGPL-3 MD5sum: 85659747d3b927c73dedf3da73b4131b NeedsCompilation: no Package: CytoGLMM Version: 1.6.0 Imports: stats, methods, BiocParallel, RColorBrewer, cowplot, doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr, mbest, pheatmap, speedglm, stringr, strucchange, tibble, ggrepel, MASS, logging, Matrix, tidyr, caret, rlang, grDevices Suggests: knitr, rmarkdown, testthat, BiocStyle License: LGPL-3 MD5sum: 6d8317453ff879d25487a41d27fd7ecb NeedsCompilation: no Package: cytoKernel Version: 1.4.0 Depends: R (>= 4.1) Imports: Rcpp, SummarizedExperiment, utils, methods, ComplexHeatmap, circlize, ashr, data.table, BiocParallel, dplyr, stats, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 162ed3a92413fd301c277f3f8b22d9b5 NeedsCompilation: yes Package: cytolib Version: 2.10.1 Depends: R (>= 3.4) Imports: RProtoBufLib LinkingTo: BH(>= 1.75.0.0), RProtoBufLib(>= 2.3.5),Rhdf5lib Suggests: knitr, rmarkdown License_restricts_use: no MD5sum: 3b158d63c5164d3f97c567325b1a8b2c NeedsCompilation: yes Package: cytomapper Version: 1.10.1 Depends: R (>= 4.0), EBImage, SingleCellExperiment, methods Imports: SpatialExperiment, S4Vectors, BiocParallel, HDF5Array, DelayedArray, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5, nnls Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest License: GPL (>= 2) MD5sum: 12b542b73613b6f0389e6be8a7cfd96f NeedsCompilation: no Package: cytoMEM Version: 1.2.0 Depends: R (>= 4.2.0) Imports: gplots, tools, flowCore, grDevices, stats, utils, matrixStats, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: df6d7a8cd1d1cee932c7f40590d5af18 NeedsCompilation: no Package: CytoML Version: 2.10.0 Depends: R (>= 3.5.0) Imports: cytolib(>= 2.3.10), flowCore (>= 1.99.10), flowWorkspace (>= 4.1.8), openCyto (>= 1.99.2), XML, data.table, jsonlite, RBGL, Rgraphviz, Biobase, methods, graph, graphics, utils, jsonlite, dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, stats, tibble LinkingTo: cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, flowWorkspace Suggests: testthat, flowWorkspaceData , knitr, rmarkdown, parallel License_restricts_use: no MD5sum: 71bcccc39f35834d4781d9bd5c7c9d2c NeedsCompilation: yes Package: dada2 Version: 1.26.0 Depends: R (>= 3.4.0), Rcpp (>= 0.12.0), methods (>= 3.4.0) Imports: Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), ShortRead (>= 1.32.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0), IRanges (>= 2.6.0), XVector (>= 0.16.0), BiocGenerics (>= 0.22.0) LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, knitr, rmarkdown License: LGPL-2 MD5sum: b633d014f891b3c096c594b976bca494 NeedsCompilation: yes Package: dagLogo Version: 1.36.0 Depends: R (>= 3.0.1), methods, grid Imports: pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils, biomaRt, motifStack, httr Suggests: XML, grImport, grImport2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 5f03fce26f9ca11e3d8121b97b9214e5 NeedsCompilation: no Package: daMA Version: 1.70.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: 0b4f775a14999125edd0cc4fe48893d2 NeedsCompilation: no Package: DAMEfinder Version: 1.10.1 Depends: R (>= 4.0) Imports: stats, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, readr, SummarizedExperiment, GenomicAlignments, stringr, plyr, VariantAnnotation, parallel, ggplot2, Rsamtools, BiocGenerics, methods, limma, bumphunter, Biostrings, reshape2, cowplot, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 9c63cc715a135654263c69f41966d329 NeedsCompilation: no Package: DaMiRseq Version: 2.10.0 Depends: R (>= 3.5.0), SummarizedExperiment, ggplot2 Imports: DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap, FactoMineR, corrplot, randomForest, e1071, caret, MASS, lubridate, plsVarSel, kknn, FSelector, methods, stats, utils, graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR, plyr Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: a69e43d1c439f138eb8fe8588f21403f NeedsCompilation: no Package: DAPAR Version: 1.30.6 Depends: R (>= 4.2.0) Imports: Biobase, MSnbase, DAPARdata (>= 1.28.0), utils, highcharter, foreach Suggests: testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph, diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR, factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster, forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr, norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr, limma, preprocessCore, stringr, tidyr, impute, gplots, grDevices, reshape2, graphics, stats, methods, ggplot2, RColorBrewer, Matrix, org.Sc.sgd.db License: Artistic-2.0 MD5sum: a32553bb8fe92274937703b8a02b5b5b NeedsCompilation: no Package: DART Version: 1.46.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: f6c156909eea46417349a2328ec138a0 NeedsCompilation: no Package: dasper Version: 1.7.0 Depends: R (>= 4.0) Imports: basilisk, BiocFileCache, BiocParallel, data.table, dplyr, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, ggpubr, ggrepel, grid, IRanges, magrittr, megadepth, methods, plyranges, readr, reticulate, rtracklayer, S4Vectors, stringr, SummarizedExperiment, tidyr Suggests: AnnotationFilter, BiocStyle, covr, ensembldb, GenomicState, knitr, lifecycle, markdown, recount, RefManageR, rmarkdown, sessioninfo, testthat, tibble License: Artistic-2.0 MD5sum: 03063c741ff942b14988308afa0d8db0 NeedsCompilation: no Package: dcanr Version: 1.14.0 Depends: R (>= 3.6.0) Imports: igraph, foreach, plyr, stringr, reshape2, methods, Matrix, graphics, stats, RColorBrewer, circlize, doRNG Suggests: EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 MD5sum: fa72b8e5f0f844eae6390577a607b88e NeedsCompilation: no Package: dce Version: 1.6.0 Depends: R (>= 4.1) Imports: stats, methods, assertthat, graph, pcalg, purrr, tidyverse, Matrix, ggraph, tidygraph, ggplot2, rlang, expm, MASS, edgeR, epiNEM, igraph, metap, mnem, naturalsort, ppcor, glm2, graphite, reshape2, dplyr, magrittr, glue, Rgraphviz, harmonicmeanp, org.Hs.eg.db, logger, shadowtext Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, cowplot, ggplotify, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment, RcppParallel, docopt, CARNIVAL License: GPL-3 MD5sum: 2d5262b4d89619cb9749b4a994c6b3aa NeedsCompilation: no Package: dcGSA Version: 1.26.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: 8cc4eb1d6217eac647ee3861091d5fb5 NeedsCompilation: no Package: ddCt Version: 1.54.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: testthat (>= 3.0.0), RUnit License: LGPL-3 MD5sum: dad22ce3a853722f1866046cfc196330 NeedsCompilation: no Package: ddPCRclust Version: 1.18.0 Depends: R (>= 3.5) Imports: plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore, flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks Suggests: BiocStyle License: Artistic-2.0 MD5sum: 6fee35cd73bf0de1310b501da8366865 NeedsCompilation: no Package: dearseq Version: 1.10.0 Depends: R (>= 3.6.0) Imports: CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr, matrixStats, methods, patchwork, parallel, pbapply, reshape2, rlang, scattermore, stats, statmod, survey, tibble, viridisLite Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr License: GPL-2 | file LICENSE MD5sum: 6e0446710c4c34c6e317fb66bc8e75b4 NeedsCompilation: no Package: debCAM Version: 1.16.0 Depends: R (>= 3.5) Imports: methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR2, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 MD5sum: f35c71fd173ba6e56cf77fafc6f839e2 NeedsCompilation: no Package: debrowser Version: 1.26.3 Depends: R (>= 3.5.0), Imports: shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT, ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE, igraph, grDevices, graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker, plotly, heatmaply, Harman, pathview, apeglm, ashr Suggests: testthat, rmarkdown, knitr License: GPL-3 + file LICENSE MD5sum: 9235cc95f042f36c9a66f412b5930f34 NeedsCompilation: no Package: DECIPHER Version: 2.26.0 Depends: R (>= 3.5.0), Biostrings (>= 2.59.1), RSQLite (>= 1.1), stats, parallel Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector License: GPL-3 MD5sum: 242d3228884db231e85fd8a0f7e2bd7d NeedsCompilation: yes Package: deco Version: 1.13.0 Depends: R (>= 3.5.0), AnnotationDbi, BiocParallel, SummarizedExperiment, limma Imports: stats, methods, ggplot2, foreign, graphics, BiocStyle, Biobase, cluster, gplots, RColorBrewer, locfit, made4, ade4, sfsmisc, scatterplot3d, gdata, grDevices, utils, reshape2, gridExtra Suggests: knitr, curatedTCGAData, MultiAssayExperiment, Homo.sapiens, rmarkdown License: GPL (>= 3) MD5sum: 2a6fcb887712cc6591e2800ed5b6f953 NeedsCompilation: no Package: DEComplexDisease Version: 1.18.0 Depends: R (>= 3.3.3) Imports: Rcpp (>= 0.12.7), DESeq2, edgeR, SummarizedExperiment, ComplexHeatmap, grid, parallel, BiocParallel, grDevices, graphics, stats, methods, utils LinkingTo: Rcpp Suggests: knitr License: GPL-3 MD5sum: 13d50403d7b5b44f1c3f40dd1adca03e NeedsCompilation: yes Package: decompTumor2Sig Version: 2.14.0 Depends: R(>= 4.0), ggplot2 Imports: methods, Matrix, quadprog(>= 1.5-5), GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table, GenomeInfoDb, readxl Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 133665fcef3a5b9762f2fc9f9f89d939 NeedsCompilation: no Package: DeconRNASeq Version: 1.40.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 MD5sum: 3ee38ccd0942a5b22c845753ccbe8d19 NeedsCompilation: no Package: decontam Version: 1.18.0 Depends: R (>= 3.4.1), methods (>= 3.4.1) Imports: ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats Suggests: BiocStyle, knitr, rmarkdown, phyloseq License: Artistic-2.0 MD5sum: b948a8d78cc9f506a0163ff386efe2b1 NeedsCompilation: no Package: deconvR Version: 1.4.3 Depends: R (>= 4.1), data.table (>= 1.14.0) Imports: S4Vectors (>= 0.30.0), methylKit (>= 1.18.0), IRanges (>= 2.26.0), GenomicRanges (>= 1.44.0), BiocGenerics (>= 0.38.0), stats, methods, foreach (>= 1.5.1), magrittr (>= 2.0.1), matrixStats (>= 0.61.0), e1071 (>= 1.7.9), quadprog (>= 1.5.8), nnls (>= 1.4), rsq (>= 2.2), MASS, utils, dplyr (>= 1.0.7), tidyr (>= 1.1.3), assertthat, minfi Suggests: testthat (>= 3.0.0), roxygen2 (>= 7.1.2), doParallel (>= 1.0.16), parallel, knitr (>= 1.34), BiocStyle (>= 2.20.2), reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), rmarkdown, devtools (>= 2.4.2), sessioninfo (>= 1.1.1), covr, granulator, RefManageR License: Artistic-2.0 MD5sum: cf6c2d0a9043360af86246e77307bcbc NeedsCompilation: no Package: decoupleR Version: 2.4.0 Depends: R (>= 4.0) Imports: broom, dplyr, magrittr, Matrix, purrr, rlang, stats, stringr, tibble, tidyr, tidyselect, withr Suggests: glmnet (>= 4.1.0), GSVA, viper, fgsea (>= 1.15.4), AUCell, SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr, pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo, pheatmap, testthat, OmnipathR, Seurat, ggplot2, ggrepel, patchwork License: GPL-3 + file LICENSE MD5sum: 5bcdf1db35f539ea6e7e32ed40e3d434 NeedsCompilation: no Package: DeepBlueR Version: 1.24.1 Depends: R (>= 3.3), XML, RCurl Imports: GenomicRanges, data.table, stringr, diffr, dplyr, methods, rjson, utils, R.utils, foreach, withr, rtracklayer, GenomeInfoDb, settings, filehash Suggests: knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr, RColorBrewer, matrixStats License: GPL (>= 2.0) MD5sum: a21ff5b6e2fb3c87eab955680dcd19e5 NeedsCompilation: no Package: DeepPINCS Version: 1.6.0 Depends: keras, R (>= 4.1) Imports: tensorflow, CatEncoders, matlab, rcdk, stringdist, tokenizers, webchem, purrr, ttgsea, PRROC, reticulate, stats Suggests: knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: cc81273ece84492a613d35dff09b5673 NeedsCompilation: no Package: deepSNV Version: 1.44.0 Depends: R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.27.6), Imports: Rhtslib LinkingTo: Rhtslib (>= 1.13.1) Suggests: RColorBrewer, knitr, rmarkdown License: GPL-3 MD5sum: 5083e5404197de4c3d29ca070d32809a NeedsCompilation: yes Package: DEFormats Version: 1.26.0 Imports: checkmate, data.table, DESeq2, edgeR (>= 3.13.4), GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat License: GPL-3 MD5sum: b61d2716b59d6a167c20c5ba5687f131 NeedsCompilation: no Package: DegNorm Version: 1.8.2 Depends: R (>= 4.0.0), methods Imports: Rcpp (>= 1.0.2),GenomicFeatures, parallel, foreach, S4Vectors, doParallel, Rsamtools (>= 1.31.2), GenomicAlignments, heatmaply, data.table, stats, ggplot2, GenomicRanges, IRanges, plyr, plotly, utils,viridis LinkingTo: Rcpp, RcppArmadillo,S4Vectors,IRanges Suggests: knitr,rmarkdown,formatR License: LGPL (>= 3) MD5sum: 8e642cec5f28196ef3ecf8a8dd76580d NeedsCompilation: yes Package: DEGraph Version: 1.50.0 Depends: R (>= 2.10.0), R.utils Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph License: GPL-3 MD5sum: f046aae8779fc9953668e819a0bce2f8 NeedsCompilation: no Package: DEGreport Version: 1.34.0 Depends: R (>= 4.0.0) Imports: utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, magrittr, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE MD5sum: 56d4240c09a51da9ca4832b8db37d61e NeedsCompilation: no Package: DEGseq Version: 1.52.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: 3634ebf8b632faa6072bc269fa987e5a NeedsCompilation: yes Package: DelayedArray Version: 0.24.0 Depends: R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>= 0.43.4), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2), IRanges (>= 2.17.3) Imports: stats LinkingTo: S4Vectors Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit License: Artistic-2.0 MD5sum: 0a80b8a189e2db3c44fda356c12b3a7c NeedsCompilation: yes Package: DelayedDataFrame Version: 1.14.0 Depends: R (>= 3.6), S4Vectors (>= 0.23.19), DelayedArray (>= 0.7.5) Imports: methods, stats, BiocGenerics Suggests: testthat, knitr, rmarkdown, SeqArray, GDSArray License: GPL-3 MD5sum: 5da143c0d548a58d283b60c389024581 NeedsCompilation: no Package: DelayedMatrixStats Version: 1.20.0 Depends: MatrixGenerics (>= 1.5.3), DelayedArray (>= 0.17.6) Imports: methods, matrixStats (>= 0.60.0), sparseMatrixStats, Matrix (>= 1.5-0), S4Vectors (>= 0.17.5), IRanges (>= 2.25.10) Suggests: testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark, profmem, HDF5Array License: MIT + file LICENSE MD5sum: eccc9b5201ff734463db9b0e453c11a0 NeedsCompilation: no Package: DelayedRandomArray Version: 1.6.0 Depends: DelayedArray Imports: methods, dqrng, Rcpp LinkingTo: dqrng, BH, Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, Matrix License: GPL-3 MD5sum: 1d7f165ed8ce1db3bb2352add74c3fdc NeedsCompilation: yes Package: DelayedTensor Version: 1.4.0 Depends: R (>= 4.1.0) Imports: methods, utils, DelayedArray, HDF5Array, BiocSingular, rTensor, DelayedRandomArray, irlba, Matrix, einsum, Suggests: markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr, dplyr, reticulate License: Artistic-2.0 MD5sum: 59b12779b3e41f042a33bee198c3ff0a NeedsCompilation: no Package: deltaCaptureC Version: 1.12.0 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2, tictoc Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: b77a952031c7d4ffde1e86a0e16956d0 NeedsCompilation: no Package: deltaGseg Version: 1.38.0 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 MD5sum: b74b63f8492cde2a21a963276bb90726 NeedsCompilation: no Package: DeMAND Version: 1.28.0 Depends: R (>= 2.14.0), KernSmooth, methods License: file LICENSE MD5sum: 7693da687af4608dc1a0db9b701c6abf NeedsCompilation: no Package: DeMixT Version: 1.14.0 Depends: R (>= 3.6.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment, knitr, KernSmooth, matrixcalc, rmarkdown, DSS, dendextend, psych, sva Imports: matrixStats, stats, truncdist, base64enc, ggplot2 LinkingTo: Rcpp License: GPL-3 MD5sum: 01d3dac06f864ac67ed2f890ee077452 NeedsCompilation: yes Package: demuxmix Version: 1.0.0 Depends: R (>= 4.0.0) Imports: stats, MASS, Matrix, ggplot2, gridExtra, methods Suggests: BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: df0284f78ff8d585e18a6d0e9410ef30 NeedsCompilation: no Package: densvis Version: 1.8.3 Imports: Rcpp, basilisk, assertthat, reticulate, irlba LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, ggplot2, Rtsne, uwot, testthat License: MIT + file LICENSE MD5sum: beebc59f0f70b475f1703a72bed7c695 NeedsCompilation: yes Package: DEP Version: 1.20.0 Depends: R (>= 3.5) Imports: ggplot2, dplyr, purrr, readr, tibble, tidyr, SummarizedExperiment (>= 1.11.5), MSnbase, limma, vsn, fdrtool, ggrepel, ComplexHeatmap, RColorBrewer, circlize, shiny, shinydashboard, DT, rmarkdown, assertthat, gridExtra, grid, stats, imputeLCMD, cluster Suggests: testthat, enrichR, knitr, BiocStyle License: Artistic-2.0 MD5sum: 6f0dd158dd403aa298b3c13fb4573b89 NeedsCompilation: no Package: DepecheR Version: 1.14.0 Depends: R (>= 4.0) Imports: ggplot2 (>= 3.1.0), MASS (>= 7.3.51), Rcpp (>= 1.0.0), dplyr (>= 0.7.8), gplots (>= 3.0.1), viridis (>= 0.5.1), foreach (>= 1.4.4), doSNOW (>= 1.0.16), matrixStats (>= 0.54.0), mixOmics (>= 6.6.1), moments (>= 0.14), grDevices (>= 3.5.2), graphics (>= 3.5.2), stats (>= 3.5.2), utils (>= 3.5), methods (>= 3.5), parallel (>= 3.5.2), reshape2 (>= 1.4.3), beanplot (>= 1.2), FNN (>= 1.1.3), robustbase (>= 0.93.5), gmodels (>= 2.18.1) LinkingTo: Rcpp, RcppEigen Suggests: uwot, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 6e69a75fc559cdaf7d8e7bd2216edb92 NeedsCompilation: yes Package: DepInfeR Version: 1.2.0 Depends: R (>= 4.2.0) Imports: matrixStats, glmnet, stats, BiocParallel Suggests: testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble, ggplot2, missForest, pheatmap, RColorBrewer, ggrepel, ggbeeswarm License: GPL-3 MD5sum: c2dd33e24fdd4f41912edfae52d1577f NeedsCompilation: no Package: DEqMS Version: 1.16.0 Depends: R(>= 3.5),graphics,stats,ggplot2,matrixStats,limma(>= 3.34) Suggests: BiocStyle,knitr,rmarkdown,markdown,plyr,reshape2,farms,utils,ggrepel,ExperimentHub,LSD License: LGPL MD5sum: 9764c93e44b7bff35cac5ab2077f6967 NeedsCompilation: no Package: derfinder Version: 1.32.0 Depends: R (>= 3.5.0) Imports: BiocGenerics (>= 0.25.1), AnnotationDbi (>= 1.27.9), BiocParallel (>= 1.15.15), bumphunter (>= 1.9.2), derfinderHelper (>= 1.1.0), GenomeInfoDb (>= 1.3.3), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges (>= 1.17.40), Hmisc, IRanges (>= 2.3.23), methods, qvalue (>= 1.99.0), Rsamtools (>= 1.25.0), rtracklayer, S4Vectors (>= 0.23.19), stats, utils Suggests: BiocStyle (>= 2.5.19), sessioninfo, derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat (>= 2.1.0), TxDb.Hsapiens.UCSC.hg19.knownGene, covr License: Artistic-2.0 MD5sum: faa523304229ab81eb54b497f6a1688d NeedsCompilation: no Package: derfinderHelper Version: 1.32.0 Depends: R(>= 3.2.2) Imports: IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2) Suggests: sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), RefManageR, rmarkdown (>= 0.3.3), testthat, covr License: Artistic-2.0 MD5sum: bba4cb39cd85594b1c413fe93b74cfaf NeedsCompilation: no Package: derfinderPlot Version: 1.32.0 Depends: R(>= 3.2) Imports: derfinder (>= 1.1.0), GenomeInfoDb (>= 1.3.3), GenomicFeatures, GenomicRanges (>= 1.17.40), ggbio (>= 1.13.13), ggplot2, graphics, grDevices, IRanges (>= 1.99.28), limma, methods, plyr, RColorBrewer, reshape2, S4Vectors (>= 0.9.38), scales, utils Suggests: biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData (>= 0.99.0), sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, RefManageR, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, covr License: Artistic-2.0 MD5sum: c0213295480ab890e7cce412f4a3a5ec NeedsCompilation: no Package: DEScan2 Version: 1.18.2 Depends: R (>= 3.5), GenomicRanges Imports: BiocParallel, BiocGenerics, ChIPpeakAnno, data.table, DelayedArray, GenomeInfoDb, GenomicAlignments, glue, IRanges, plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors (>= 0.23.19), SummarizedExperiment, tools, utils LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod License: Artistic-2.0 MD5sum: d8c674a2e22ca2b4b3f7043769b2ff41 NeedsCompilation: yes Package: DESeq2 Version: 1.38.3 Depends: S4Vectors (>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, matrixStats, methods, stats4, locfit, geneplotter, ggplot2, Rcpp (>= 0.11.0) LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10), glmGamPoi, BiocManager License: LGPL (>= 3) MD5sum: 32379516b8531b9b0f8c908815b529e5 NeedsCompilation: yes Package: DEsingle Version: 1.18.1 Depends: R (>= 3.4.0) Imports: stats, Matrix (>= 1.2-14), MASS (>= 7.3-45), VGAM (>= 1.0-2), bbmle (>= 1.0.18), gamlss (>= 4.4-0), maxLik (>= 1.3-4), pscl (>= 1.4.9), BiocParallel (>= 1.12.0), Suggests: knitr, rmarkdown, SingleCellExperiment License: GPL-2 MD5sum: 3c5cc66ebebb721c89d63f01a0c4785c NeedsCompilation: no Package: destiny Version: 3.12.0 Depends: R (>= 3.4.0) Imports: methods, graphics, grDevices, grid, utils, stats, Matrix, Rcpp (>= 0.10.3), RcppEigen, RSpectra (>= 0.14-0), irlba, pcaMethods, Biobase, BiocGenerics, SummarizedExperiment, SingleCellExperiment, ggplot2, ggplot.multistats, tidyr, tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW, smoother, scales, scatterplot3d LinkingTo: Rcpp, RcppEigen, grDevices Suggests: knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, org.Mm.eg.db, scran, repr Enhances: rgl, SingleCellExperiment License: GPL-3 MD5sum: 2f7c3e52c683d657357fa82fe26fecc9 NeedsCompilation: yes Package: DEsubs Version: 1.24.0 Depends: R (>= 3.3), locfit Imports: graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq, stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix, jsonlite, tools, DESeq2, methods Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL-3 MD5sum: d20fca4a4429eb812e661ddbd780a502 NeedsCompilation: no Package: DEWSeq Version: 1.12.0 Depends: R(>= 4.0.0), R.utils, DESeq2, BiocParallel Imports: BiocGenerics, data.table(>= 1.11.8), GenomeInfoDb, GenomicRanges, methods, S4Vectors, SummarizedExperiment, stats, utils Suggests: knitr, rmarkdown, testthat, BiocStyle, IHW License: LGPL (>= 3) MD5sum: 7eef7adc0d6eed7e109664578f0a7c53 NeedsCompilation: no Package: DExMA Version: 1.6.0 Depends: R (>= 4.1), DExMAdata Imports: Biobase, GEOquery, impute, limma, pheatmap, plyr, scales, snpStats, sva, swamp, stats, methods, utils, bnstruct, RColorBrewer, grDevices Suggests: BiocStyle, qpdf, BiocGenerics, RUnit License: GPL-2 MD5sum: 8463b6f8020f8b47f21d2b8d0519b70a NeedsCompilation: no Package: DEXSeq Version: 1.44.0 Depends: BiocParallel, Biobase, SummarizedExperiment, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), DESeq2 (>= 1.9.11), AnnotationDbi, RColorBrewer, S4Vectors (>= 0.23.18) Imports: BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter Suggests: GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 3) MD5sum: b18982d6f7bd08e3302900292b9f674c NeedsCompilation: no Package: DFP Version: 1.56.0 Depends: methods, Biobase (>= 2.5.5) License: GPL-2 MD5sum: d6b76195d7950f5e9575d7595d85cb77 NeedsCompilation: no Package: DIAlignR Version: 2.6.0 Depends: methods, stats, R (>= 4.0) Imports: zoo (>= 1.8-3), data.table, magrittr, dplyr, tidyr, rlang, mzR (>= 2.18), signal, bit64, reticulate, ggplot2, RSQLite, DBI, ape, phangorn, pracma, RMSNumpress, Rcpp LinkingTo: Rcpp, RcppEigen Suggests: knitr, akima, lattice, scales, gridExtra, latticeExtra, rmarkdown, BiocStyle, BiocParallel, testthat (>= 2.1.0) License: GPL-3 MD5sum: 64c32812c3ee3739d1224ded108e6413 NeedsCompilation: yes Package: DiffBind Version: 3.8.4 Depends: R (>= 4.0), GenomicRanges, SummarizedExperiment Imports: RColorBrewer, amap, gplots, grDevices, limma, GenomicAlignments, locfit, stats, utils, IRanges, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools (>= 2.13.1), DESeq2, methods, graphics, ggrepel, apeglm, ashr, GreyListChIP LinkingTo: Rhtslib (>= 1.99.1), Rcpp Suggests: BiocStyle, testthat, xtable Enhances: rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid License: Artistic-2.0 MD5sum: 537d2734861f3cfde272740f49686ac8 NeedsCompilation: yes Package: diffcoexp Version: 1.18.0 Depends: R (>= 3.5), WGCNA, SummarizedExperiment Imports: stats, DiffCorr, psych, igraph, BiocGenerics Suggests: GEOquery License: GPL (> 2) MD5sum: 78d716ed9922ad37828872406c5d393a NeedsCompilation: no Package: diffcyt Version: 1.18.0 Depends: R (>= 3.4.0) Imports: flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma, edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats, methods, utils, grDevices, graphics, ComplexHeatmap, circlize, grid Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST License: MIT + file LICENSE MD5sum: 24de43c96ac3fdecd877ca028e0c5fc6 NeedsCompilation: no Package: DifferentialRegulation Version: 1.2.2 Depends: R (>= 4.2.0) Imports: methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, stats, BANDITS, Matrix, SingleCellExperiment, SummarizedExperiment, ggplot2 LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: a60791bd49cfc2f26f54d6de3bd6a988 NeedsCompilation: yes Package: diffGeneAnalysis Version: 1.80.0 Imports: graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils License: GPL MD5sum: 9320cdacf623ed2c00860bfc7cecb4ec NeedsCompilation: no Package: diffHic Version: 1.30.0 Depends: R (>= 3.5), GenomicRanges, InteractionSet, SummarizedExperiment Imports: Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma, csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb, BiocGenerics, grDevices, graphics, stats, utils, Rcpp, rtracklayer LinkingTo: Rhtslib (>= 1.13.1), zlibbioc, Rcpp Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix, testthat License: GPL-3 MD5sum: b9b86e15e59038edb1ab1c879aa8dab6 NeedsCompilation: yes Package: DiffLogo Version: 2.22.0 Depends: R (>= 3.4), stats, cba Imports: grDevices, graphics, utils, tools Suggests: knitr, testthat, seqLogo, MotifDb License: GPL (>= 2) MD5sum: e2367dc8dff7b85a5d1456f86081294b NeedsCompilation: no Package: diffuStats Version: 1.18.0 Depends: R (>= 3.4) Imports: grDevices, stats, methods, Matrix, MASS, checkmate, expm, igraph, Rcpp, RcppArmadillo, RcppParallel, plyr, precrec LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2, utils License: GPL-3 MD5sum: 99deeec6c2c90480bb2a6bce8e4b059a NeedsCompilation: yes Package: diffUTR Version: 1.6.0 Depends: R (>= 4.0) Imports: S4Vectors, SummarizedExperiment, limma, edgeR, DEXSeq, GenomicRanges, Rsubread, ggplot2, rtracklayer, ComplexHeatmap, ggrepel, stringi, methods, stats, GenomeInfoDb, dplyr, matrixStats, IRanges, ensembldb, viridisLite Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: d389e262756575825cb3fd1e87f7da23 NeedsCompilation: no Package: diggit Version: 1.30.0 Depends: R (>= 3.0.2), Biobase, methods Imports: ks, viper(>= 1.3.1), parallel Suggests: diggitdata License: file LICENSE MD5sum: e22c732b2ce65822d5030e772df924f4 NeedsCompilation: no Package: Dino Version: 1.4.0 Depends: R (>= 4.0.0) Imports: BiocParallel, BiocSingular, SummarizedExperiment, SingleCellExperiment, S4Vectors, Matrix, Seurat, matrixStats, parallel, scran, grDevices, stats, methods Suggests: testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools, ggplot2, gridExtra, ggpubr, grid, magick, hexbin License: GPL-3 MD5sum: 66671d63510b7ea7ef08ce31f006c4b0 NeedsCompilation: no Package: dir.expiry Version: 1.6.0 Imports: utils, filelock Suggests: rmarkdown, knitr, testthat, BiocStyle License: GPL-3 MD5sum: 8b0a798316a94942d17161f2ca4b6e99 NeedsCompilation: no Package: Director Version: 1.24.0 Depends: R (>= 4.0) Imports: htmltools, utils, grDevices License: GPL-3 + file LICENSE MD5sum: 0d4cae3747a23c79ea450c290edf75c3 NeedsCompilation: no Package: DirichletMultinomial Version: 1.40.0 Depends: S4Vectors, IRanges Imports: stats4, methods, BiocGenerics Suggests: lattice, parallel, MASS, RColorBrewer, xtable License: LGPL-3 MD5sum: 2aef6ee52884858b31172b63d0930cfe NeedsCompilation: yes Package: discordant Version: 1.22.0 Depends: R (>= 4.1.0) Imports: Rcpp, Biobase, stats, biwt, gtools, MASS, tools, dplyr, methods, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 6df3ea65dc1532d8541e81e6c7bf55fd NeedsCompilation: yes Package: DiscoRhythm Version: 1.14.0 Depends: R (>= 3.6.0) Imports: matrixTests, matrixStats, MetaCycle (>= 1.2.0), data.table, ggplot2, ggExtra, dplyr, broom, shiny, shinyBS, shinycssloaders, shinydashboard, shinyjs, BiocStyle, rmarkdown, knitr, kableExtra, magick, VennDiagram, UpSetR, heatmaply, viridis, plotly, DT, gridExtra, methods, stats, SummarizedExperiment, BiocGenerics, S4Vectors, zip, reshape2 Suggests: testthat License: GPL-3 MD5sum: 1b7c9a6697e18dd9a924a26647265153 NeedsCompilation: no Package: distinct Version: 1.10.2 Depends: R (>= 4.0) Imports: Rcpp, Rfast, stats, SummarizedExperiment, SingleCellExperiment, methods, Matrix, foreach, parallel, doParallel, doRNG, ggplot2, limma, scater LinkingTo: Rcpp, RcppArmadillo, Rfast Suggests: knitr, rmarkdown, testthat, UpSetR License: GPL (>= 3) MD5sum: 41db57ea276847d4181d4601d0efed49 NeedsCompilation: yes Package: dittoSeq Version: 1.10.0 Depends: ggplot2 Imports: methods, colorspace (>= 1.4), gridExtra, cowplot, reshape2, pheatmap, grDevices, ggrepel, ggridges, stats, utils, SummarizedExperiment, SingleCellExperiment, S4Vectors Suggests: plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR, ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran License: MIT + file LICENSE MD5sum: edf7aed33d56c9592a8ae6c09b43acdb NeedsCompilation: no Package: divergence Version: 1.14.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown License: GPL-2 MD5sum: b27d40897e1210656095c96a388f8f45 NeedsCompilation: no Package: dks Version: 1.44.0 Depends: R (>= 2.8) Imports: cubature License: GPL MD5sum: d93ca0629aabccf5f42958777ba341c9 NeedsCompilation: no Package: DMCFB Version: 1.12.0 Depends: R (>= 4.0.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges Imports: utils, stats, speedglm, MASS, data.table, splines, arm, rtracklayer, benchmarkme, tibble, matrixStats, fastDummies, graphics Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 4c76de9be414900aadbead2a0f42c306 NeedsCompilation: no Package: DMCHMM Version: 1.20.0 Depends: R (>= 4.1.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges, fdrtool Imports: utils, stats, grDevices, rtracklayer, multcomp, calibrate, graphics Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: b9834c4cf269d8dcb74790e4e8dbf13e NeedsCompilation: no Package: DMRcaller Version: 1.30.0 Depends: R (>= 3.5), GenomicRanges, IRanges, S4Vectors (>= 0.23.10) Imports: parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 5b51c7d79dafa39c1d841eaa21e144be NeedsCompilation: no Package: DMRcate Version: 2.12.0 Depends: R (>= 4.0.0) Imports: ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, DSS, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment Suggests: knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata License: file LICENSE MD5sum: fcc418be3d20a5d98ada6656124573fe NeedsCompilation: no Package: DMRforPairs Version: 1.34.0 Depends: R (>= 2.15.2), Gviz (>= 1.2.1), R2HTML (>= 2.2.1), GenomicRanges (>= 1.10.7), parallel License: GPL (>= 2) MD5sum: 3ad83c7ea0408bda0133d22d96c190ca NeedsCompilation: no Package: DMRScan Version: 1.20.0 Depends: R (>= 3.6.0) Imports: Matrix, MASS, RcppRoll,GenomicRanges, IRanges, GenomeInfoDb, methods, mvtnorm, stats, parallel Suggests: knitr, rmarkdown, BiocStyle, BiocManager License: GPL-3 MD5sum: 7b65d7c47a659b314a0491bd008e8d34 NeedsCompilation: no Package: dmrseq Version: 1.18.1 Depends: R (>= 3.5), bsseq Imports: GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer, bumphunter, DelayedMatrixStats (>= 1.1.13), matrixStats, BiocParallel, outliers, methods, locfit, IRanges, grDevices, graphics, stats, utils, annotatr, AnnotationHub, rtracklayer, GenomeInfoDb, splines Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: c62f42c90821a15765f5ff88424f55a7 NeedsCompilation: no Package: DNABarcodeCompatibility Version: 1.14.0 Depends: R (>= 3.6.0) Imports: dplyr, tidyr, numbers, purrr, stringr, DNABarcodes, stats, utils, methods Suggests: knitr, rmarkdown, BiocStyle, testthat License: file LICENSE MD5sum: 1027a9cb369deb4a38828f51fc97632e NeedsCompilation: no Package: DNABarcodes Version: 1.28.0 Depends: Matrix, parallel Imports: Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, BiocStyle, rmarkdown License: GPL-2 MD5sum: 7a7fb3d4f03a9eaa574a81d96e3e256a NeedsCompilation: yes Package: DNAcopy Version: 1.72.3 License: GPL (>= 2) MD5sum: aa91303bfd470ab11bf34b06259d7288 NeedsCompilation: yes Package: DNAfusion Version: 1.0.0 Depends: R (>= 4.2.0) Imports: bamsignals, GenomicRanges, IRanges, Rsamtools, GenomicAlignments, BiocBaseUtils, S4Vectors Suggests: knitr, rmarkdown, testthat, sessioninfo, BiocStyle, License: GPL-3 MD5sum: 2a902d457521f1ebf8b2ca36163dd2de NeedsCompilation: no Package: DNAshapeR Version: 1.26.0 Depends: R (>= 3.4), GenomicRanges Imports: Rcpp (>= 0.12.1), Biostrings, fields LinkingTo: Rcpp Suggests: AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret License: GPL-2 MD5sum: 44687dd0152a4bfeb6d072ede8a9a217 NeedsCompilation: yes Package: DominoEffect Version: 1.18.0 Depends: R(>= 3.5) Imports: biomaRt, data.table, utils, stats, Biostrings, SummarizedExperiment, VariantAnnotation, AnnotationDbi, GenomeInfoDb, IRanges, GenomicRanges, methods Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: b1da1141e9d2bd2f763c6297bce3f6e7 NeedsCompilation: no Package: doppelgangR Version: 1.26.0 Depends: R (>= 3.5.0), Biobase, BiocParallel Imports: sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat License: GPL (>= 2.0) MD5sum: 959dd9827864db89ef05d4acd526ad48 NeedsCompilation: no Package: Doscheda Version: 1.20.0 Depends: R (>= 3.4) Imports: methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy, limma, stringr, ggplot2, graphics, grDevices, calibrate, corrgram, gridExtra, DT, shiny, shinydashboard, readxl, prodlim, matrixStats Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: feed2c10c258627119453f847e763272 NeedsCompilation: no Package: DOSE Version: 3.24.2 Depends: R (>= 3.5.0) Imports: AnnotationDbi, HDO.db, BiocParallel, fgsea, ggplot2, GOSemSim (>= 2.23.1), methods, qvalue, reshape2, stats, utils Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, rmarkdown, org.Hs.eg.db, testthat License: Artistic-2.0 MD5sum: 391363330b411ea31dd262e04df50906 NeedsCompilation: no Package: doseR Version: 1.14.0 Depends: R (>= 3.6) Imports: edgeR, methods, stats, graphics, matrixStats, mclust, lme4, RUnit, SummarizedExperiment, digest, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: ec35228d655a89d682235837377a65dd NeedsCompilation: no Package: dpeak Version: 1.10.0 Depends: R (>= 4.0.0), methods, stats, utils, graphics, Rcpp Imports: MASS, IRanges, BSgenome, grDevices, parallel LinkingTo: Rcpp Suggests: BSgenome.Ecoli.NCBI.20080805 License: GPL (>= 2) MD5sum: 5c0ae9cedec6e3cda0b4b772542d7bcc NeedsCompilation: yes Package: drawProteins Version: 1.18.0 Depends: R (>= 4.0) Imports: ggplot2, httr, dplyr, readr, tidyr Suggests: covr, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 0f7c383d5df708ec3512eea75b68bb51 NeedsCompilation: no Package: DRIMSeq Version: 1.26.0 Depends: R (>= 3.4.0) Imports: utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2 Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: b0e7a537d5ba56b9ab59319bd2be27a9 NeedsCompilation: no Package: DriverNet Version: 1.38.0 Depends: R (>= 2.10), methods License: GPL-3 MD5sum: 24bd5a77d291fdb8b80c5f803f029723 NeedsCompilation: no Package: DropletUtils Version: 1.18.1 Depends: SingleCellExperiment Imports: utils, stats, methods, Matrix, Rcpp, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiocParallel, DelayedArray, DelayedMatrixStats, HDF5Array, rhdf5, edgeR, R.utils, dqrng, beachmat, scuttle LinkingTo: Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle Suggests: testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles License: GPL-3 MD5sum: 8b6dd84250172d53cfbb6636141d878a NeedsCompilation: yes Package: drugTargetInteractions Version: 1.6.0 Depends: methods, R (>= 4.1) Imports: utils, RSQLite, UniProt.ws, biomaRt,ensembldb, BiocFileCache,dplyr,rappdirs, AnnotationFilter, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT, EnsDb.Hsapiens.v86 License: Artistic-2.0 MD5sum: eb80ddd832c35d54f7ef7043992ebe86 NeedsCompilation: no Package: DrugVsDisease Version: 2.40.0 Depends: R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery, DrugVsDiseasedata, cMap2data, qvalue Imports: annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit, BiocGenerics, xtable License: GPL-3 MD5sum: babca2ebe58102cc744de3a80f95d137 NeedsCompilation: no Package: DSS Version: 2.46.0 Depends: R (>= 3.5.0), methods, Biobase, BiocParallel, bsseq, parallel Imports: utils, graphics, stats, splines Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: cfddb2dffe867e04864458103ddc4c4a NeedsCompilation: yes Package: dStruct Version: 1.4.0 Depends: R (>= 4.1) Imports: zoo, ggplot2, purrr, reshape2, parallel, IRanges, S4Vectors, rlang, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 4f42240b3ddd43ddedb8e69401ebd174 NeedsCompilation: no Package: DTA Version: 2.44.0 Depends: R (>= 2.10), LSD Imports: scatterplot3d License: Artistic-2.0 MD5sum: 5d3d9632d873e5f491d36556611da276 NeedsCompilation: no Package: Dune Version: 1.10.0 Depends: R (>= 3.6) Imports: BiocParallel, SummarizedExperiment, utils, ggplot2, dplyr, tidyr, RColorBrewer, magrittr, gganimate, purrr, aricode Suggests: knitr, rmarkdown, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 2b6f8892515c68f0858b9ad9ed793bd3 NeedsCompilation: no Package: dupRadar Version: 1.28.0 Depends: R (>= 3.2.0) Imports: Rsubread (>= 1.14.1), KernSmooth Suggests: BiocStyle, knitr, rmarkdown, AnnotationHub License: GPL-3 MD5sum: ba6eac4a78d4ce96708daba439896483 NeedsCompilation: no Package: dyebias Version: 1.58.0 Depends: R (>= 1.4.1), marray, Biobase Suggests: limma, convert, GEOquery, dyebiasexamples, methods License: GPL-3 MD5sum: ebed952e1115f00b803eea21caf15aeb NeedsCompilation: no Package: DynDoc Version: 1.76.0 Depends: methods, utils Imports: methods License: Artistic-2.0 MD5sum: f7d5391c485c725b42c217246de82443 NeedsCompilation: no Package: easier Version: 1.4.0 Depends: R (>= 4.2.0) Imports: progeny, easierData, dorothea (>= 1.6.0), quantiseqr, ROCR, grDevices, stats, graphics, ggplot2, ggpubr, DESeq2, utils, dplyr, matrixStats, rlang, BiocParallel, reshape2, rstatix, ggrepel, coin Suggests: knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment License: MIT + file LICENSE MD5sum: 27caa6b42f2c3e59e83c02f0707ab2e0 NeedsCompilation: no Package: EasyCellType Version: 1.0.0 Depends: R (>= 4.2.0) Imports: clusterProfiler, dplyr, forcats, ggplot2, magrittr, rlang, stats, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi Suggests: knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools License: Artistic-2.0 MD5sum: 647eb1bfd87c25f865e266a17328cd66 NeedsCompilation: no Package: easyreporting Version: 1.10.0 Depends: R (>= 3.5.0) Imports: rmarkdown, methods, tools, shiny, rlang Suggests: distill, BiocStyle, knitr, readxl, edgeR, limma, EDASeq, statmod License: Artistic-2.0 MD5sum: 5e2a0fca97c00157d1a6f06367cbccd1 NeedsCompilation: no Package: easyRNASeq Version: 2.34.0 Imports: Biobase (>= 2.50.0), BiocFileCache (>= 1.14.0), BiocGenerics (>= 0.36.0), BiocParallel (>= 1.24.1), biomaRt (>= 2.46.0), Biostrings (>= 2.58.0), edgeR (>= 3.32.0), GenomeInfoDb (>= 1.26.0), genomeIntervals (>= 1.46.0), GenomicAlignments (>= 1.26.0), GenomicRanges (>= 1.42.0), SummarizedExperiment (>= 1.20.0), graphics, IRanges (>= 2.24.0), LSD (>= 4.1-0), locfit, methods, parallel, rappdirs (>= 0.3.1), Rsamtools (>= 2.6.0), S4Vectors (>= 0.28.0), ShortRead (>= 1.48.0), utils Suggests: BiocStyle (>= 2.18.0), BSgenome (>= 1.58.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.32) License: Artistic-2.0 MD5sum: 9cbf39467a416d27084288899332bb0b NeedsCompilation: no Package: EBarrays Version: 2.62.0 Depends: R (>= 1.8.0), Biobase, lattice, methods Imports: Biobase, cluster, graphics, grDevices, lattice, methods, stats License: GPL (>= 2) MD5sum: 37e657ffd76a71420a26ce30a2f162e8 NeedsCompilation: yes Package: EBcoexpress Version: 1.42.0 Depends: EBarrays, mclust, minqa Suggests: graph, igraph, colorspace License: GPL (>= 2) MD5sum: e43fedf0e0c05dc3ea92c68cd5218570 NeedsCompilation: yes Package: EBImage Version: 4.40.0 Depends: methods Imports: BiocGenerics (>= 0.7.1), graphics, grDevices, stats, abind, tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils, htmltools, htmlwidgets, RCurl Suggests: BiocStyle, digest, knitr, rmarkdown, shiny License: LGPL MD5sum: f879fa92a5c9e8ee2ba935191c6b983d NeedsCompilation: yes Package: EBSEA Version: 1.26.0 Depends: R (>= 4.0.0) Imports: DESeq2, graphics, stats, EmpiricalBrownsMethod Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 7055b7242a27748eafee7c00087f5c29 NeedsCompilation: no Package: EBSeq Version: 1.38.0 Depends: blockmodeling, gplots, testthat, R (>= 3.0.0) License: Artistic-2.0 MD5sum: 3dcbccf3dab22b82b2535991266b3f02 NeedsCompilation: no Package: EBSeqHMM Version: 1.32.0 Depends: EBSeq License: Artistic-2.0 MD5sum: f91eb234118df0f141ecf9e6c80dc7cf NeedsCompilation: no Package: ecolitk Version: 1.70.0 Depends: R (>= 2.10) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy License: GPL (>= 2) MD5sum: b90afffa63497e4f37db7757beb5667c NeedsCompilation: no Package: EDASeq Version: 2.32.0 Depends: Biobase (>= 2.15.1), ShortRead (>= 1.11.42) Imports: methods, graphics, BiocGenerics, IRanges (>= 1.13.9), aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings, AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager Suggests: BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat, DESeq2, rmarkdown License: Artistic-2.0 MD5sum: 948506096325abacab298979c0e9e958 NeedsCompilation: no Package: edge Version: 2.30.0 Depends: R(>= 3.1.0), Biobase Imports: methods, splines, sva, snm, qvalue(>= 1.99.0), MASS Suggests: testthat, knitr, ggplot2, reshape2 License: MIT + file LICENSE MD5sum: d1d99a3666fc3f05f226e739e7fb8760 NeedsCompilation: yes Package: edgeR Version: 3.40.2 Depends: R (>= 3.6.0), limma (>= 3.41.5) Imports: methods, graphics, stats, utils, locfit, Rcpp LinkingTo: Rcpp Suggests: jsonlite, readr, rhdf5, splines, Biobase, AnnotationDbi, SummarizedExperiment, org.Hs.eg.db License: GPL (>= 2) MD5sum: c6cd5f896a43e7c9b896e61a4e2a9f5f NeedsCompilation: yes Package: eds Version: 1.0.0 Depends: Matrix Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, tximportData, testthat (>= 3.0.0) License: GPL-2 MD5sum: 85c6bd1320b354b1227103894175f6b9 NeedsCompilation: yes Package: eegc Version: 1.24.0 Depends: R (>= 3.4.0) Imports: R.utils, gplots, sna, wordcloud, igraph, pheatmap, edgeR, DESeq2, clusterProfiler, S4Vectors, ggplot2, org.Hs.eg.db, org.Mm.eg.db, limma, DOSE, AnnotationDbi Suggests: knitr License: GPL-2 MD5sum: a01830ae30002de8ea33d9306518e007 NeedsCompilation: no Package: EGAD Version: 1.26.0 Depends: R(>= 3.5) Imports: gplots, Biobase, GEOquery, limma, impute, RColorBrewer, zoo, igraph, plyr, MASS, RCurl, methods Suggests: knitr, testthat, rmarkdown, markdown License: GPL-2 MD5sum: 1269c359e66dbd7a6528ebe3fc414d25 NeedsCompilation: no Package: EGSEA Version: 1.26.0 Depends: R (>= 3.5), Biobase, gage (>= 2.14.4), AnnotationDbi, topGO (>= 2.16.0), pathview (>= 1.4.2) Imports: PADOG (>= 1.6.0), GSVA (>= 1.12.0), globaltest (>= 5.18.0), limma (>= 3.20.9), edgeR (>= 3.6.8), HTMLUtils (>= 0.1.5), hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0), safe (>= 3.4.0), stringi (>= 0.5.0), parallel, stats, metap, grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, RColorBrewer, methods, EGSEAdata (>= 1.3.1), htmlwidgets, plotly, DT Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: ec031d870897e310bebdfc7f5109b73c NeedsCompilation: no Package: eiR Version: 1.38.0 Depends: R (>= 2.10.0), ChemmineR (>= 2.15.15), methods, DBI Imports: snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl, digest, BiocGenerics, RcppAnnoy (>= 0.0.9) Suggests: BiocStyle, knitcitations, knitr, knitrBootstrap,rmarkdown License: Artistic-2.0 MD5sum: 4fff518f3b66ce1d8b47b75702e53a00 NeedsCompilation: yes Package: eisaR Version: 1.10.0 Depends: R (>= 4.1) Imports: graphics, stats, GenomicRanges, S4Vectors, IRanges, limma, edgeR, methods, SummarizedExperiment, BiocGenerics, utils Suggests: knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, rtracklayer License: GPL-3 MD5sum: b92d1bf994bf18cd43607b386db578a5 NeedsCompilation: no Package: ELMER Version: 2.22.0 Depends: R (>= 3.4.0), ELMER.data (>= 2.9.3) Imports: GenomicRanges, ggplot2, reshape, grid, grDevices, graphics, methods, parallel, stats, utils, IRanges, GenomeInfoDb, S4Vectors, GenomicFeatures, TCGAbiolinks (>= 2.23.7), plyr, Matrix, dplyr, Gviz, ComplexHeatmap, circlize, MultiAssayExperiment, SummarizedExperiment, biomaRt, doParallel, downloader, ggrepel, lattice, magrittr, readr, scales, rvest, xml2, plotly, gridExtra, rmarkdown, stringr, tibble, tidyr, progress, purrr, reshape2, ggpubr, rtracklayer, DelayedArray Suggests: BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData License: GPL-3 MD5sum: 40c2d94b6db36145eb8de725ab0ad16b NeedsCompilation: no Package: EMDomics Version: 2.28.0 Depends: R (>= 3.2.1) Imports: emdist, BiocParallel, matrixStats, ggplot2, CDFt, preprocessCore Suggests: knitr License: MIT + file LICENSE MD5sum: c7785eaa643af4a1846b2fb9c1345497 NeedsCompilation: no Package: EmpiricalBrownsMethod Version: 1.26.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: d0796abd0422744d6a42ed1fc7150552 NeedsCompilation: no Package: EnhancedVolcano Version: 1.16.0 Depends: ggplot2, ggrepel Imports: methods Suggests: ggalt, ggrastr, RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway, org.Hs.eg.db, gridExtra, magrittr, rmarkdown License: GPL-3 MD5sum: 54bfc2e0610cc542ac705867353e6113 NeedsCompilation: no Package: enhancerHomologSearch Version: 1.4.2 Depends: R (>= 4.1.0), methods Imports: BiocGenerics, Biostrings, BSgenome, BiocParallel, BiocFileCache, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, motifmatchr, Matrix, rtracklayer, Rcpp, S4Vectors, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, MotifDb, testthat, TFBSTools License: GPL (>= 2) MD5sum: c766049e598a26492da9470fd86439d7 NeedsCompilation: yes Package: ENmix Version: 1.34.02 Depends: R (>= 3.5.0), parallel, doParallel, foreach, SummarizedExperiment, stats Imports: grDevices,graphics,preprocessCore,matrixStats,methods,utils, geneplotter,impute,minfi,RPMM,illuminaio,dynamicTreeCut,IRanges,gtools, Biobase,ExperimentHub,AnnotationHub,genefilter,gplots,quadprog,S4Vectors Suggests: minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 97ffa721d92d8c52739f56c7eec8fb44 NeedsCompilation: no Package: EnrichedHeatmap Version: 1.28.1 Depends: R (>= 3.6.0), methods, grid, ComplexHeatmap (>= 2.11.0), GenomicRanges Imports: matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize (>= 0.4.5), IRanges LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter, RColorBrewer License: MIT + file LICENSE MD5sum: f52dcfa3183fea87ce02bd7dff0ad8ae NeedsCompilation: yes Package: EnrichmentBrowser Version: 2.28.2 Depends: SummarizedExperiment, graph Imports: AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR, graphite, hwriter, limma, methods, pathview, safe Suggests: ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown License: Artistic-2.0 MD5sum: 116eb27a4c41ceb5949e0bb6c9957c01 NeedsCompilation: no Package: enrichplot Version: 1.18.4 Depends: R (>= 3.5.0) Imports: aplot (>= 0.1.4), DOSE (>= 3.16.0), ggnewscale, ggplot2, ggraph, graphics, grid, igraph, methods, plyr, purrr, RColorBrewer, reshape2, rlang, stats, utils, scatterpie, shadowtext, GOSemSim, magrittr, ggtree, yulab.utils (>= 0.0.4) Suggests: clusterProfiler, dplyr, europepmc, ggupset, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggrepel (>= 0.9.0), ggstar, treeio, scales, tidytree, ggtreeExtra, tidydr License: Artistic-2.0 MD5sum: f8ad4bab77c4354bf8aca57692df2c1b NeedsCompilation: no Package: enrichTF Version: 1.14.0 Depends: pipeFrame Imports: BSgenome, rtracklayer, motifmatchr, TFBSTools, R.utils, methods, JASPAR2018, GenomeInfoDb, GenomicRanges, IRanges, BiocGenerics, S4Vectors, utils, parallel, stats, ggpubr, heatmap3, ggplot2, clusterProfiler, rmarkdown, grDevices, magrittr Suggests: knitr, testthat, webshot License: GPL-3 MD5sum: e8e6f8eecf3fdec5b9e6e29a1022647e NeedsCompilation: no Package: ensembldb Version: 2.22.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.31.18), GenomicFeatures (>= 1.49.6), AnnotationFilter (>= 1.5.2) Imports: methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb, AnnotationDbi (>= 1.31.19), rtracklayer, S4Vectors (>= 0.23.10), Rsamtools, IRanges (>= 2.13.24), ProtGenerics, Biostrings (>= 2.47.9), curl Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), magrittr, rmarkdown, AnnotationHub Enhances: RMariaDB, shiny License: LGPL MD5sum: 59d5563c58f14888b07507513e12fdf3 NeedsCompilation: no Package: ensemblVEP Version: 1.40.0 Depends: methods, BiocGenerics, GenomicRanges, VariantAnnotation Imports: S4Vectors (>= 0.9.25), Biostrings, SummarizedExperiment, GenomeInfoDb, stats Suggests: RUnit License: Artistic-2.0 MD5sum: c637c93267812afc223745b033ea95c5 NeedsCompilation: no Package: epialleleR Version: 1.6.1 Depends: R (>= 4.1) Imports: stats, methods, utils, GenomicRanges, BiocGenerics, GenomeInfoDb, SummarizedExperiment, VariantAnnotation, stringi, data.table, Rcpp LinkingTo: Rcpp, BH, Rhtslib, zlibbioc Suggests: RUnit, knitr, rmarkdown, ggplot2, ggstance, gridExtra License: Artistic-2.0 MD5sum: 4f1ada3aab291db95f429375b4885d66 NeedsCompilation: yes Package: EpiCompare Version: 1.2.0 Depends: R (>= 4.1.0) Imports: AnnotationHub, BRGenomics, ChIPseeker, data.table, genomation, GenomicRanges, IRanges, GenomeInfoDb, ggplot2, htmltools, methods, plotly, reshape2, rmarkdown, rtracklayer, stats, stringr, utils, BiocGenerics Suggests: badger, BiocFileCache, BiocParallel, parallel, BiocStyle, clusterProfiler, GenomicAlignments, grDevices, htmlwidgets, knitr, org.Hs.eg.db, testthat (>= 3.0.0), tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, UpSetR, plyranges, scales, Matrix, consensusSeekeR License: GPL-3 MD5sum: 0dc68e72644aa43c811046b2ed3ae5ec NeedsCompilation: no Package: epidecodeR Version: 1.6.0 Depends: R (>= 3.1.0) Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr Suggests: knitr, rmarkdown License: GPL-3 MD5sum: ba98fc51a7f5aed3da968fa40faca816 NeedsCompilation: no Package: EpiDISH Version: 2.14.1 Depends: R (>= 4.1) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat License: GPL-2 MD5sum: 4d5ee3cc189547a6aa761363ef0632c2 NeedsCompilation: no Package: epigenomix Version: 1.38.0 Depends: R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment Imports: BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray License: LGPL-3 MD5sum: 7a886d5f5da9650c322dcf82f697648f NeedsCompilation: no Package: epigraHMM Version: 1.6.4 Depends: R (>= 3.5.0) Imports: Rcpp, magrittr, data.table, SummarizedExperiment, methods, GenomeInfoDb, GenomicRanges, rtracklayer, IRanges, Rsamtools, bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5, Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap, grDevices LinkingTo: Rcpp, RcppArmadillo, Rhdf5lib Suggests: testthat, knitr, rmarkdown, BiocStyle, BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData License: MIT + file LICENSE MD5sum: 59f9ba44ea3db58427058f12b52f2a94 NeedsCompilation: yes Package: epihet Version: 1.13.0 Depends: R(>= 3.6), GenomicRanges, IRanges, S4Vectors, ggplot2, foreach, Rtsne, igraph Imports: data.table, doParallel, EntropyExplorer, graphics, stats, grDevices, pheatmap, utils, qvalue, WGCNA, ReactomePA Suggests: knitr, clusterProfiler, ggfortify, org.Hs.eg.db, rmarkdown License: Artistic-2.0 MD5sum: 26b1e6d8404649e2cafdbfbff19a2805 NeedsCompilation: no Package: EpiMix Version: 1.0.1 Depends: R (>= 4.2.0), EpiMix.data (>= 0.99.2) Imports: AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table, doParallel, doSNOW, downloader, dplyr, ELMER.data, ExperimentHub, foreach, GenomeInfoDb, GenomicFeatures, GenomicRanges, GEOquery, ggplot2, graphics, grDevices, impute, IRanges, limma, methods, parallel, plyr, progress, R.matlab, RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, utils Suggests: BiocStyle, clusterProfiler, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics License: GPL-3 MD5sum: 0efebd22c87fa4a4f29707c8e613d2f7 NeedsCompilation: no Package: epimutacions Version: 1.2.0 Depends: R (>= 4.2.0), epimutacionsData Imports: minfi, bumphunter, isotree, robustbase, ggplot2, GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment, stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt, BiocParallel, GenomeInfoDb, Homo.sapiens, purrr, tibble, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, AnnotationDbi, AnnotationHub, ExperimentHub, reshape2, grid, ensembldb, gridExtra, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, ggrepel Suggests: testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices License: MIT + file LICENSE MD5sum: 51f420dc23c3131fc644f4462bd99793 NeedsCompilation: yes Package: epiNEM Version: 1.22.0 Depends: R (>= 4.1) Imports: BoolNet, e1071, gtools, stats, igraph, utils, lattice, latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph, mnem, latex2exp Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db License: GPL-3 MD5sum: a9264cbf5edec4ad27ecdf189366fcd3 NeedsCompilation: no Package: epistack Version: 1.4.0 Depends: R (>= 4.1) Imports: GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, viridisLite, graphics, plotrix, grDevices, stats, methods Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick License: MIT + file LICENSE MD5sum: e5d8ace460efb0bbb035794209180bf3 NeedsCompilation: no Package: epistasisGA Version: 1.0.2 Depends: R (>= 4.0) Imports: BiocParallel, data.table, matrixStats, stats, survival, igraph, batchtools, qgraph, grDevices, parallel, Rcpp (>= 0.11.0), ggplot2, grid, graphics, utils LinkingTo: Rcpp, RcppArmadillo Suggests: Matrix, BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0) License: GPL-3 MD5sum: 1222ff801ba141fddd152970c6623aff NeedsCompilation: yes Package: EpiTxDb Version: 1.10.0 Depends: R (>= 4.0), AnnotationDbi, Modstrings Imports: methods, utils, httr, xml2, curl, GenomicFeatures, GenomicRanges, GenomeInfoDb, BiocGenerics, BiocFileCache, S4Vectors, IRanges, RSQLite, DBI, Biostrings, tRNAdbImport Suggests: BiocStyle, knitr, rmarkdown, testthat, httptest, AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: 4461aeaecb08c8025776e81737d5f5c3 NeedsCompilation: no Package: epivizr Version: 2.28.0 Depends: R (>= 3.5.0), methods Imports: epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4), GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown License: Artistic-2.0 MD5sum: 4e64b3fe2ee9c4ba3c11a80ca868634e NeedsCompilation: no Package: epivizrChart Version: 1.20.0 Depends: R (>= 3.5.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub License: Artistic-2.0 MD5sum: 505b4fb5b026abd9754c631f58c62f9c NeedsCompilation: no Package: epivizrData Version: 1.26.0 Depends: R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase Imports: S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0), OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats License: MIT + file LICENSE MD5sum: c208f72e3255905f13d292b740f5a70e NeedsCompilation: no Package: epivizrServer Version: 1.26.0 Depends: R (>= 3.2.3), methods Imports: httpuv (>= 1.3.0), R6 (>= 2.0.0), rjson, mime (>= 0.2) Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: b396fa1c9286bece2671aeb8827d154c NeedsCompilation: no Package: epivizrStandalone Version: 1.26.0 Depends: R (>= 3.2.3), epivizr (>= 2.3.6), methods Imports: git2r, epivizrServer, GenomeInfoDb, BiocGenerics, GenomicFeatures, S4Vectors Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle License: MIT + file LICENSE MD5sum: b4f345553fbeb8376970f8d3aad418d0 NeedsCompilation: no Package: erccdashboard Version: 1.32.0 Depends: R (>= 3.2), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0) Imports: edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr, qvalue, reshape2, ROCR, scales, stringr License: GPL (>= 2) MD5sum: ba26cc07920c686e3010e7bbed975d3e NeedsCompilation: no Package: erma Version: 1.14.0 Depends: R (>= 3.1), methods, Homo.sapiens, GenomicFiles (>= 1.5.2) Imports: rtracklayer (>= 1.38.1), S4Vectors (>= 0.23.18), BiocGenerics, GenomicRanges, SummarizedExperiment, ggplot2, GenomeInfoDb, Biobase, shiny, BiocParallel, IRanges, AnnotationDbi Suggests: rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel License: Artistic-2.0 MD5sum: 5811fca20ad2fce297e69eb2bfe15776 NeedsCompilation: no Package: ERSSA Version: 1.16.0 Depends: R (>= 4.0.0) Imports: edgeR (>= 3.23.3), DESeq2 (>= 1.21.16), ggplot2 (>= 3.0.0), RColorBrewer (>= 1.1-2), plyr (>= 1.8.4), BiocParallel (>= 1.15.8), grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 6af7e20eb2f76d86d1af1b2eb03721e7 NeedsCompilation: no Package: esATAC Version: 1.20.0 Depends: R (>= 4.0.0), Rsamtools, GenomicRanges, ShortRead, pipeFrame Imports: Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer, ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph, rJava, magrittr, digest, BSgenome, AnnotationDbi, GenomicAlignments, GenomicFeatures, R.utils, GenomeInfoDb, BiocGenerics, S4Vectors, IRanges, rmarkdown, tools, VennDiagram, grid, JASPAR2018, TFBSTools, grDevices, graphics, stats, utils, parallel, corrplot, BiocManager, motifmatchr LinkingTo: Rcpp Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat, webshot License: GPL-3 | file LICENSE Archs: x64 MD5sum: 0665935ec59a7dc0d13a89a2a7aee2b4 NeedsCompilation: yes Package: escape Version: 1.8.0 Depends: R (>= 4.1) Imports: grDevices, dplyr, ggplot2, GSEABase, GSVA, SingleCellExperiment, ggridges, msigdbr, stats, BiocParallel, Matrix, UCell, broom, reshape2, patchwork, MatrixGenerics, utils, rlang, stringr, data.table, SummarizedExperiment, methods Suggests: Seurat, SeuratObject, knitr, rmarkdown, markdown, BiocStyle, testthat, dittoSeq (>= 1.1.2) License: GPL-2 MD5sum: fddfcbb4f063e9d8db08427bdba86222 NeedsCompilation: no Package: esetVis Version: 1.24.0 Imports: mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils, grDevices, methods Suggests: ggplot2, ggvis, rbokeh, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment License: GPL-3 MD5sum: c7fb116c6d1b27829af8d7e4db990211 NeedsCompilation: no Package: eudysbiome Version: 1.28.0 Depends: R (>= 3.1.0) Imports: plyr, Rsamtools, R.utils, Biostrings License: GPL-2 MD5sum: 9170c603e9591dcb733041fe8d592bb7 NeedsCompilation: no Package: evaluomeR Version: 1.14.0 Depends: R (>= 3.6), SummarizedExperiment, MultiAssayExperiment, cluster (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14), flexmix (>= 2.3.15) Imports: corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2, ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class, prabclus, mclust, kableExtra Suggests: BiocStyle, knitr, rmarkdown, magrittr License: GPL-3 MD5sum: 8abc37b5da285307f8f50debec7ee2ec NeedsCompilation: no Package: EventPointer Version: 3.6.0 Depends: R (>= 3.5.0), SGSeq, Matrix, SummarizedExperiment Imports: GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls, limma, matrixStats, RBGL, prodlim, graph, methods, utils, stats, doParallel, foreach, affxparser, GenomicRanges, S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome, Biostrings, glmnet, abind, iterators, lpSolve, poibin, speedglm, tximport, fgsea Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra License: Artistic-2.0 MD5sum: 7fb6b64c68081a77a4a83b502227aac7 NeedsCompilation: yes Package: EWCE Version: 1.6.0 Depends: R (>= 4.2), RNOmni (>= 1.0) Imports: stats, utils, methods, ewceData, dplyr, ggplot2, reshape2, limma, stringr, HGNChelper, Matrix, parallel, SingleCellExperiment, SummarizedExperiment, DelayedArray, BiocParallel, orthogene (>= 0.99.8), data.table Suggests: remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, cowplot, ggdendro, grDevices, grid, gridExtra, scales, magick, badger License: GPL-3 MD5sum: 9c76425eadd916e87b3c8de9b1ab7edf NeedsCompilation: no Package: ExCluster Version: 1.16.0 Depends: Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges Imports: stats, methods, grDevices, graphics, utils License: GPL-3 MD5sum: 0d23af311ba618053d8b5d5df320f72f NeedsCompilation: no Package: ExiMiR Version: 2.40.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.26.1), limma Imports: affyio(>= 1.13.3), Biobase(>= 2.5.5), preprocessCore(>= 1.10.0) Suggests: mirna10cdf License: GPL-2 MD5sum: c08d694578905c778ccb49e9c2c7d181 NeedsCompilation: no Package: exomeCopy Version: 1.44.0 Depends: R (>= 3.5.0), IRanges (>= 2.5.27), GenomicRanges (>= 1.23.16), Rsamtools Imports: stats4, methods, GenomeInfoDb Suggests: Biostrings License: GPL (>= 2) MD5sum: 6a07931c4b2acae6d052add5468327b0 NeedsCompilation: yes Package: exomePeak2 Version: 1.10.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: Rsamtools,GenomicAlignments,GenomicRanges,GenomicFeatures,DESeq2,ggplot2,mclust,BSgenome,Biostrings,GenomeInfoDb,BiocParallel,IRanges,S4Vectors,rtracklayer,methods,stats,utils,BiocGenerics,magrittr,speedglm,splines Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: c96e499f822a2522298910a4666d4b0e NeedsCompilation: no Package: ExperimentHub Version: 2.6.0 Depends: methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 3.3.6), BiocFileCache (>= 1.5.1) Imports: utils, S4Vectors, BiocManager, curl, rappdirs Suggests: knitr, BiocStyle, rmarkdown, HubPub Enhances: ExperimentHubData License: Artistic-2.0 MD5sum: cc5c46814f9be117919fabc695236536 NeedsCompilation: no Package: ExperimentHubData Version: 1.24.0 Depends: utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData (>= 1.21.3) Imports: methods, ExperimentHub, BiocManager, DBI, httr, curl Suggests: GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown, HubPub License: Artistic-2.0 MD5sum: 2f65f3ee496fdb31fc16ec7df76b1d51 NeedsCompilation: no Package: ExperimentSubset Version: 1.8.0 Depends: R (>= 4.0.0), SummarizedExperiment, SingleCellExperiment, SpatialExperiment, TreeSummarizedExperiment Imports: methods, Matrix, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran, scater, scds, TENxPBMCData, airway License: MIT + file LICENSE MD5sum: dbdbc776b2ec7e46b0a8b4ec3d008aec NeedsCompilation: no Package: ExploreModelMatrix Version: 1.10.0 Imports: shiny (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr, magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales, tibble, MASS, limma, S4Vectors, shinyjs Suggests: testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle License: MIT + file LICENSE MD5sum: 84a19578e29e250ad50b26a54395590b NeedsCompilation: no Package: ExpressionAtlas Version: 1.26.0 Depends: R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2, RCurl, jsonlite, BiocStyle Imports: utils, XML, httr Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: 273ee1d201e69a395000f7e5a03bcc86 NeedsCompilation: no Package: extraChIPs Version: 1.2.4 Depends: BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 3.4.0), SummarizedExperiment, tibble Imports: BiocIO, broom, ComplexUpset, csaw, dplyr, edgeR, EnrichedHeatmap, forcats, GenomeInfoDb, GenomicInteractions, ggforce, ggrepel, ggside, glue, grDevices, grid, Gviz, InteractionSet, IRanges, limma, methods, patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales, stats, stringr, tidyr, tidyselect, utils, vctrs, VennDiagram Suggests: BiocStyle, covr, knitr, plyranges, rmarkdown, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: 20d18e1b4583982a117710e5fa238cd8 NeedsCompilation: no Package: fabia Version: 2.44.0 Depends: R (>= 3.6.0), Biobase Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: 3b0753dffdaf9332be82ef728ea6414a NeedsCompilation: yes Package: factDesign Version: 1.74.0 Depends: Biobase (>= 2.5.5) Imports: stats Suggests: affy, genefilter, multtest License: LGPL MD5sum: ba540a009ae24b291d138ef205640b0d NeedsCompilation: no Package: factR Version: 1.0.0 Depends: R (>= 4.2) Imports: BiocGenerics (>= 0.38), Biostrings (>= 2.60), GenomeInfoDb (>= 1.28), dplyr (>= 1.0), GenomicFeatures (>= 1.44), GenomicRanges (>= 1.44), IRanges (>= 2.26), purrr (>= 0.3), rtracklayer (>= 1.52), tidyr (>= 1.1), methods (>= 4.0), BiocParallel (>= 1.26), S4Vectors (>= 0.30), data.table (>= 1.14), rlang (>= 1.0), tibble (>= 3.1), wiggleplotr (>= 1.16), RCurl (>= 1.98), XML (>= 3.99), drawProteins (>= 1.12), ggplot2 (>= 3.3), stringr (>= 1.4), pbapply (>= 1.5), stats (>= 4.1), utils (>= 4.1), graphics (>= 4.1), crayon Suggests: AnnotationHub (>= 2.22), BSgenome (>= 1.58), BSgenome.Mmusculus.UCSC.mm10, testthat, knitr, rmarkdown, markdown, zeallot, rmdformats, bio3d (>= 2.4), signalHsmm (>= 1.5), tidyverse (>= 1.3), covr, patchwork License: file LICENSE MD5sum: 4f90c7ad11f87c93b01a1492a1e37cfd NeedsCompilation: no Package: FamAgg Version: 1.26.0 Depends: methods, kinship2, igraph Imports: gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey Suggests: BiocStyle, knitr, RUnit, rmarkdown License: MIT + file LICENSE MD5sum: 0dee07a5e9b0bdfd570eb92869e28611 NeedsCompilation: no Package: famat Version: 1.8.0 Depends: R (>= 4.0) Imports: KEGGREST, mgcv, stats, BiasedUrn, dplyr, gprofiler2, rWikiPathways, reactome.db, stringr, GO.db, ontologyIndex, tidyr, shiny, shinydashboard, shinyBS, plotly, magrittr, DT, clusterProfiler, org.Hs.eg.db Suggests: BiocStyle, knitr, rmarkdown, testthat, BiocManager License: GPL-3 MD5sum: ed39234859b59bb3d5e8d0f4f24e455d NeedsCompilation: no Package: farms Version: 1.50.0 Depends: R (>= 2.8), affy (>= 1.20.0), MASS, methods Imports: affy, MASS, Biobase (>= 1.13.41), methods, graphics Suggests: affydata, Biobase, utils License: LGPL (>= 2.1) MD5sum: e154bc07ef63234d2ebdcaba01eb7fef NeedsCompilation: no Package: fastLiquidAssociation Version: 1.34.0 Depends: methods, LiquidAssociation, parallel, doParallel, stats, Hmisc, utils Imports: WGCNA, impute, preprocessCore Suggests: GOstats, yeastCC, org.Sc.sgd.db License: GPL-2 MD5sum: 38c9d0564f95b3cf8823705497a16535 NeedsCompilation: no Package: FastqCleaner Version: 1.16.1 Imports: methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12) LinkingTo: Rcpp Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: d2d61c57b3016966083679f62f4edab0 NeedsCompilation: yes Package: fastreeR Version: 1.2.0 Depends: R (>= 4.2) Imports: ape, data.table, dynamicTreeCut, methods, R.utils, rJava, stats, stringr, utils Suggests: BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: ed3789e9e124a893ee0a864f4fb7c665 NeedsCompilation: no Package: fastseg Version: 1.44.0 Depends: R (>= 2.13), GenomicRanges, Biobase Imports: methods, graphics, grDevices, stats, BiocGenerics, S4Vectors, IRanges Suggests: DNAcopy, oligo License: LGPL (>= 2.0) MD5sum: 742e53847386ac1b4950cac18671540b NeedsCompilation: yes Package: FCBF Version: 2.6.0 Depends: R (>= 4.1) Imports: ggplot2, gridExtra, pbapply, parallel, SummarizedExperiment, stats, mclust Suggests: caret, mlbench, SingleCellExperiment, knitr, rmarkdown, testthat, BiocManager License: MIT + file LICENSE MD5sum: f703ec2896ce7597244b6b92a4d8695c NeedsCompilation: no Package: fCCAC Version: 1.24.0 Depends: R (>= 4.2.0), S4Vectors, IRanges, GenomicRanges, grid Imports: fda, RColorBrewer, genomation, ggplot2, ComplexHeatmap, grDevices, stats, utils Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 40f92c91b3f32744695923e826213be6 NeedsCompilation: no Package: fCI Version: 1.28.0 Depends: R (>= 3.1),FNN, psych, gtools, zoo, rgl, grid, VennDiagram Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: d69351cf103efa256887b07336f30a06 NeedsCompilation: no Package: fcoex Version: 1.12.0 Depends: R (>= 4.1) Imports: FCBF, parallel, progress, dplyr, ggplot2, ggrepel, igraph, grid, intergraph, stringr, clusterProfiler, data.table, grDevices, methods, network, scales, sna, utils, stats, SingleCellExperiment, pathwayPCA, Matrix Suggests: testthat (>= 2.1.0), devtools, BiocManager, TENxPBMCData, scater, schex, gridExtra, scran, Seurat, knitr, rmarkdown License: GPL-3 MD5sum: 991b740c85ca970c5cb7d151f64a66cb NeedsCompilation: no Package: fcScan Version: 1.12.0 Imports: stats, plyr, VariantAnnotation, SummarizedExperiment, rtracklayer, GenomicRanges, methods, IRanges, foreach, doParallel, parallel Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: a21e23e957d67e52d469e39923943a41 NeedsCompilation: no Package: fdrame Version: 1.70.0 Imports: tcltk, graphics, grDevices, stats, utils License: GPL (>= 2) MD5sum: 696dbf3518ceecbcb973414a78bac8ad NeedsCompilation: yes Package: FEAST Version: 1.6.0 Depends: R (>= 4.1), mclust, BiocParallel, SummarizedExperiment Imports: SingleCellExperiment, methods, stats, utils, irlba, TSCAN, SC3, matrixStats Suggests: rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-2 MD5sum: 473ff100cae5da4d4a70140afa11c23f NeedsCompilation: yes Package: fedup Version: 1.6.0 Depends: R (>= 4.1) Imports: openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes, forcats, RColorBrewer, RCy3, utils, stats Suggests: biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr License: MIT + file LICENSE MD5sum: a7a9f5314c3a19e37117a9a6466ed309 NeedsCompilation: no Package: FELLA Version: 1.18.0 Depends: R (>= 3.5.0) Imports: methods, igraph, Matrix, KEGGREST, plyr, stats, graphics, utils Suggests: shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim License: GPL-3 MD5sum: e8d98d7a33791934d19d2eebb85daeda NeedsCompilation: no Package: ffpe Version: 1.42.0 Depends: R (>= 2.10.0), TTR, methods Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc Suggests: genefilter, ffpeExampleData License: GPL (> 2) MD5sum: 3c382d38f15d52056b1a187351c92425 NeedsCompilation: no Package: fgga Version: 1.6.0 Depends: R (>= 4.2), RBGL Imports: graph, stats, e1071, methods, gRbase, jsonlite, BiocFileCache, curl Suggests: knitr, rmarkdown, GOstats, GO.db, BiocGenerics, pROC, RUnit License: GPL-3 MD5sum: 04686fdcbc15d0e1aeaff8ef2dd1f506 NeedsCompilation: no Package: FGNet Version: 3.32.0 Depends: R (>= 4.2.0) Imports: igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2, RColorBrewer, png, methods, stats, utils, graphics, grDevices Suggests: RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, BiocManager License: GPL (>= 2) MD5sum: b956ee3f3a91f134a72306569866e427 NeedsCompilation: no Package: fgsea Version: 1.24.0 Depends: R (>= 3.3) Imports: Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), cowplot, grid, fastmatch, Matrix, utils LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation License: MIT + file LICENCE MD5sum: 37e277c0b49d3a5f3a63eb4b67198f6f NeedsCompilation: yes Package: FilterFFPE Version: 1.8.0 Imports: foreach, doParallel, GenomicRanges, IRanges, Rsamtools, parallel, S4Vectors Suggests: BiocStyle License: LGPL-3 MD5sum: 3972408b3f471a3b2a1f3ef92f216dba NeedsCompilation: no Package: FindIT2 Version: 1.4.0 Depends: GenomicRanges, R (>= 3.5.0) Imports: withr, BiocGenerics, GenomeInfoDb, rtracklayer, S4Vectors, GenomicFeatures, dplyr, rlang, patchwork, ggplot2, BiocParallel, qvalue, stringr, utils, stats, ggrepel, tibble, tidyr, SummarizedExperiment, MultiAssayExperiment, IRanges, progress, purrr, glmnet, methods Suggests: BiocStyle, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), TxDb.Athaliana.BioMart.plantsmart28 License: Artistic-2.0 MD5sum: 38324cdd6b7b7472f1760b673cff6afc NeedsCompilation: no Package: FISHalyseR Version: 1.32.0 Depends: EBImage,abind Suggests: knitr License: Artistic-2.0 MD5sum: b01ff39be83b70873833243630128e03 NeedsCompilation: no Package: fishpond Version: 2.4.1 Imports: graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, IRanges, SummarizedExperiment, GenomicRanges, matrixStats, svMisc, Matrix, SingleCellExperiment, jsonlite Suggests: testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma, ensembldb, EnsDb.Hsapiens.v86, GenomicFeatures, AnnotationDbi, pheatmap, Gviz, GenomeInfoDb, data.table License: GPL-2 MD5sum: 8d2465f38ef496a08732fd304262b4b9 NeedsCompilation: no Package: FitHiC Version: 1.24.0 Imports: data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: cb43eee3f381868b27ec04d8011884d7 NeedsCompilation: yes Package: flagme Version: 1.54.0 Depends: gcspikelite, xcms, CAMERA Imports: gplots, graphics, MASS, methods, SparseM, stats, utils License: LGPL (>= 2) MD5sum: 61eeef8f8bf05e52871aed22768e8fed NeedsCompilation: yes Package: FLAMES Version: 1.4.3 Imports: basilisk, bambu, Biostrings, BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, DropletUtils, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, ggbio, grid, gridExtra, igraph, jsonlite, magrittr, Matrix, parallel, reticulate, Rsamtools, rtracklayer, RColorBrewer, SingleCellExperiment, SummarizedExperiment, scater, S4Vectors, scuttle, stats, scran, stringr, MultiAssayExperiment, tidyr, utils, withr, zlibbioc, LinkingTo: Rcpp, Rhtslib, zlibbioc Suggests: BiocStyle, GEOquery, knitr, rmarkdown, markdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 2cb9449a0e23ba2971d7175e8a4958b0 NeedsCompilation: yes Package: flowAI Version: 1.28.0 Depends: R (>= 3.6) Imports: ggplot2, flowCore, plyr, changepoint, knitr, reshape2, RColorBrewer, scales, methods, graphics, stats, utils, rmarkdown Suggests: testthat, shiny, BiocStyle License: GPL (>= 2) MD5sum: 963544898f16672a580c8c7e87829231 NeedsCompilation: no Package: flowBeads Version: 1.36.0 Depends: R (>= 2.15.0), methods, Biobase, rrcov, flowCore Imports: flowCore, rrcov, knitr, xtable Suggests: flowViz License: Artistic-2.0 MD5sum: d8c9b095aa6fc139fd07c21ee4faefa3 NeedsCompilation: no Package: flowBin Version: 1.34.0 Depends: methods, flowCore, flowFP, R (>= 2.10) Imports: class, limma, snow, BiocGenerics Suggests: parallel License: Artistic-2.0 MD5sum: 113e74d35b74596e0c74bcfc31ffc13e NeedsCompilation: no Package: flowcatchR Version: 1.32.0 Depends: R (>= 2.10), methods, EBImage Imports: colorRamps, abind, BiocParallel, graphics, stats, utils, plotly, shiny Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 3d936fd21353498347aab0feeab24631 NeedsCompilation: no Package: flowCHIC Version: 1.32.0 Depends: R (>= 3.1.0) Imports: methods, flowCore, EBImage, vegan, hexbin, ggplot2, grid License: GPL-2 MD5sum: 1a1423c88a0f1967b2e8490cf85eea52 NeedsCompilation: no Package: flowCL Version: 1.35.0 Depends: R (>= 3.4), Rgraphviz, SPARQL Imports: methods, grDevices, utils, graph Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 44bac9a5839ae8754c782b2dbbc15629 NeedsCompilation: no Package: flowClean Version: 1.36.0 Depends: R (>= 2.15.0), flowCore Imports: bit, changepoint, sfsmisc Suggests: flowViz, grid, gridExtra License: Artistic-2.0 MD5sum: 880c4b1aafaf6116571bb449e16e0158 NeedsCompilation: no Package: flowClust Version: 3.36.1 Depends: R(>= 2.5.0) Imports: BiocGenerics, methods, Biobase, graph, flowCore, parallel Suggests: testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown, openCyto, flowStats(>= 4.7.1) License: MIT MD5sum: 4cfc7d8ea7b0168c1d77ba35eda094cd NeedsCompilation: yes Package: flowCore Version: 2.10.0 Depends: R (>= 3.5.0) Imports: Biobase, BiocGenerics (>= 0.29.2), grDevices, graphics, methods, stats, utils, stats4, Rcpp, matrixStats, cytolib (>= 2.3.4), S4Vectors LinkingTo: cpp11, BH(>= 1.65.0.1), cytolib, RProtoBufLib Suggests: Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat, flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto, gridExtra License: Artistic-2.0 MD5sum: 99d7336ef628e6fdd738ab402256c89c NeedsCompilation: yes Package: flowCut Version: 1.8.0 Depends: R (>= 3.4), flowCore Imports: flowDensity (>= 1.13.1), Cairo, e1071, grDevices, graphics, stats,methods Suggests: RUnit, BiocGenerics, knitr, markdown, rmarkdown License: Artistic-2.0 MD5sum: 1fd2359cf57c55a553f2bd9d62f555ad NeedsCompilation: no Package: flowCyBar Version: 1.34.0 Depends: R (>= 3.0.0) Imports: gplots, vegan, methods License: GPL-2 MD5sum: 5cd2e7c69f7f2feea82a7d55d9a3281e NeedsCompilation: no Package: flowDensity Version: 1.32.0 Imports: flowCore, graphics, flowViz (>= 1.46.1), car, sp, rgeos, gplots, RFOC, flowWorkspace (>= 3.33.1), methods, stats, grDevices Suggests: knitr,rmarkdown License: Artistic-2.0 MD5sum: 952a56806427a23ad1d916a6da3c9f04 NeedsCompilation: no Package: flowFP Version: 1.56.3 Depends: R (>= 2.10), flowCore, flowViz Imports: Biobase, BiocGenerics (>= 0.1.6), graphics, grDevices, methods, stats, stats4 Suggests: RUnit License: Artistic-2.0 MD5sum: 19693e8d4165b98c681e1adc829806e5 NeedsCompilation: yes Package: flowGraph Version: 1.6.0 Depends: R (>= 4.1) Imports: effsize, furrr, future, purrr, ggiraph, ggrepel, ggplot2, igraph, Matrix, matrixStats, stats, utils, visNetwork, htmlwidgets, grDevices, methods, stringr, stringi, Rdpack, data.table (>= 1.9.5), gridExtra, Suggests: BiocStyle, dplyr, knitr, rmarkdown, testthat (>= 2.1.0) License: Artistic-2.0 MD5sum: ca3c410472371c976e9d0f9053a74e9b NeedsCompilation: no Package: flowMap Version: 1.36.0 Depends: R (>= 3.0.1), ade4(>= 1.5-2), doParallel(>= 1.0.3), abind(>= 1.4.0), reshape2(>= 1.2.2), scales(>= 0.2.3), Matrix(>= 1.1-4), methods (>= 2.14) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: 7ae50f8906ce6125a68b9063d5bde05b NeedsCompilation: no Package: flowMatch Version: 1.34.0 Depends: R (>= 3.0.0), Rcpp (>= 0.11.0), methods, flowCore Imports: Biobase LinkingTo: Rcpp Suggests: healthyFlowData License: Artistic-2.0 MD5sum: 0cd3ce3d9d540276f1a898a67db45912 NeedsCompilation: yes Package: flowMeans Version: 1.58.0 Depends: R (>= 2.10.0) Imports: Biobase, graphics, grDevices, methods, rrcov, stats, feature, flowCore License: Artistic-2.0 MD5sum: 795b8d4d8018030f6ac50e5b221767df NeedsCompilation: no Package: flowMerge Version: 2.46.0 Depends: graph,feature,flowClust,Rgraphviz,foreach,snow Imports: rrcov,flowCore, graphics, methods, stats, utils Suggests: knitr, rmarkdown Enhances: doMC, multicore License: Artistic-2.0 MD5sum: 83ff08da04abc47e77f4abdea2204352 NeedsCompilation: no Package: flowPeaks Version: 1.44.0 Depends: R (>= 2.12.0) Enhances: flowCore License: Artistic-1.0 MD5sum: 41ed6b2b0dfe9d2c59b26025e441a204 NeedsCompilation: yes Package: flowPloidy Version: 1.24.0 Imports: flowCore, car, caTools, knitr, rmarkdown, minpack.lm, shiny, methods, graphics, stats, utils Suggests: flowPloidyData, testthat License: GPL-3 MD5sum: a7de42c8ef95740b57b180c4e6a1697e NeedsCompilation: no Package: flowPlots Version: 1.46.0 Depends: R (>= 2.13.0), methods Suggests: vcd License: Artistic-2.0 MD5sum: d669fc443f8e16f07beb2ec0ab92b4ba NeedsCompilation: no Package: FlowSOM Version: 2.6.0 Depends: R (>= 4.0), igraph Imports: stats, utils, colorRamps, ConsensusClusterPlus, dplyr, flowCore, ggforce, ggnewscale, ggplot2, ggpubr, grDevices, magrittr, methods, rlang, Rtsne, tidyr, BiocGenerics, XML Suggests: BiocStyle, testthat, CytoML, flowWorkspace, ggrepel, scattermore, pheatmap, ggpointdensity License: GPL (>= 2) MD5sum: a2f46b1c88174605c22c98b2103d7cee NeedsCompilation: yes Package: flowSpecs Version: 1.12.0 Depends: R (>= 4.0) Imports: ggplot2 (>= 3.1.0), BiocGenerics (>= 0.30.0), BiocParallel (>= 1.18.1), Biobase (>= 2.48.0), reshape2 (>= 1.4.3), flowCore (>= 1.50.0), zoo (>= 1.8.6), stats (>= 3.6.0), methods (>= 3.6.0) Suggests: testthat, knitr, rmarkdown, BiocStyle, DepecheR License: MIT + file LICENSE MD5sum: 2cf3ac4b436dddd4394ce557c75d9a5d NeedsCompilation: no Package: flowStats Version: 4.10.0 Depends: R (>= 3.0.2) Imports: BiocGenerics, MASS, flowCore (>= 1.99.6), flowWorkspace, ncdfFlow(>= 2.19.5), flowViz, fda (>= 2.2.6), Biobase, methods, grDevices, graphics, stats, cluster, utils, KernSmooth, lattice, ks, RColorBrewer, rrcov, corpcor, mnormt Suggests: xtable, testthat, openCyto, ggcyto, ggridges Enhances: RBGL,graph License: Artistic-2.0 MD5sum: b4abf02b574012875424458cb8d153e5 NeedsCompilation: no Package: flowTime Version: 1.22.2 Depends: R (>= 3.4), flowCore Imports: utils, dplyr (>= 1.0.0), tibble, magrittr, plyr, rlang Suggests: knitr, rmarkdown, ggplot2, BiocGenerics, stats, flowClust License: Artistic-2.0 MD5sum: d9a0c1f89c1cc0485809b359cc6224ee NeedsCompilation: no Package: flowTrans Version: 1.50.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 MD5sum: e7e0b2e4efe10276a6860b2577881e03 NeedsCompilation: no Package: flowViz Version: 1.62.0 Depends: R (>= 2.7.0), flowCore(>= 1.41.9), lattice Imports: stats4, Biobase, flowCore, graphics, grDevices, grid, KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer, stats, utils, hexbin,IDPmisc Suggests: colorspace, flowStats, knitr, rmarkdown, markdown, testthat License: Artistic-2.0 MD5sum: 6a49c31044f9ca71be913c31fde0b248 NeedsCompilation: no Package: flowVS Version: 1.30.0 Depends: R (>= 3.2), methods, flowCore, flowViz, flowStats Suggests: knitr, vsn, License: Artistic-2.0 MD5sum: 9df3dc083f106a0e963c7e6a1fcc7fc4 NeedsCompilation: no Package: flowWorkspace Version: 4.10.1 Depends: R (>= 3.5.0) Imports: Biobase, BiocGenerics, cytolib (>= 2.3.9), XML, ggplot2, graph, graphics, grDevices, methods, stats, stats4, utils, RBGL, tools, Rgraphviz, data.table, dplyr, scales, matrixStats, RProtoBufLib, flowCore(>= 2.1.1), ncdfFlow(>= 2.25.4), DelayedArray, S4Vectors LinkingTo: cpp11, BH(>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib (>= 2.3.7),Rhdf5lib Suggests: testthat, flowWorkspaceData (>= 2.23.2), knitr, rmarkdown, ggcyto, parallel, CytoML, openCyto License_restricts_use: no MD5sum: c3bf8a69c2659fe56f9643026fd3cc6b NeedsCompilation: yes Package: fmcsR Version: 1.40.0 Depends: R (>= 2.10.0), ChemmineR, methods Imports: RUnit, methods, ChemmineR, BiocGenerics, parallel Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap,rmarkdown License: Artistic-2.0 MD5sum: 5049f2dd0a203e32da67e0c5c2d5c06b NeedsCompilation: yes Package: fmrs Version: 1.8.0 Depends: R (>= 4.1.0) Imports: methods, survival, stats Suggests: BiocGenerics, testthat, knitr, utils License: GPL-3 MD5sum: edc06e391710c1670de1721d830779f9 NeedsCompilation: yes Package: fobitools Version: 1.6.0 Depends: R (>= 4.1) Imports: clisymbols, crayon, dplyr, fgsea, ggplot2, ggraph, magrittr, ontologyIndex, purrr, RecordLinkage, stringr, textclean, tictoc, tidygraph, tidyr, vroom Suggests: BiocStyle, covr, ggrepel, kableExtra, knitr, metabolomicsWorkbenchR, POMA, rmarkdown, rvest, SummarizedExperiment, testthat (>= 2.3.2), tidyverse License: GPL-3 MD5sum: aa300176fb8fee2c5592a9373ff76345 NeedsCompilation: no Package: FoldGO Version: 1.16.0 Depends: R (>= 4.0) Imports: topGO (>= 2.30.1), ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), stats, methods Suggests: knitr, rmarkdown, devtools, kableExtra License: GPL-3 MD5sum: 7a2afedbc5428ea48f0f86bc2e05312a NeedsCompilation: no Package: FRASER Version: 1.10.2 Depends: BiocParallel, data.table, Rsamtools, SummarizedExperiment Imports: AnnotationDbi, BBmisc, Biobase, BiocGenerics, biomaRt, BSgenome, cowplot, DelayedArray (>= 0.5.11), DelayedMatrixStats, extraDistr, generics, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges, grDevices, ggplot2, ggrepel, HDF5Array, matrixStats, methods, OUTRIDER, pcaMethods, pheatmap, plotly, PRROC, RColorBrewer, rhdf5, Rsubread, R.utils, S4Vectors, stats, tibble, tools, utils, VGAM LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, License: MIT + file LICENSE MD5sum: 636b41c1d73d8d59e45376736913cd50 NeedsCompilation: yes Package: frenchFISH Version: 1.10.0 Imports: utils, MCMCpack, NHPoisson Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: c321cd5a6d5a058187e136e35a8fcfe5 NeedsCompilation: no Package: FRGEpistasis Version: 1.34.0 Depends: R (>= 2.15), MASS, fda, methods, stats Imports: utils License: GPL-2 MD5sum: e0b30a5d8c3d78473741c303ec5baebb NeedsCompilation: no Package: frma Version: 1.50.0 Depends: R (>= 2.10.0), Biobase (>= 2.6.0) Imports: Biobase, MASS, DBI, affy, methods, oligo, oligoClasses, preprocessCore, utils, BiocGenerics Suggests: hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: 33285e71ae493c2296d35ea957fb302a NeedsCompilation: no Package: frmaTools Version: 1.50.0 Depends: R (>= 2.10.0), affy Imports: Biobase, DBI, methods, preprocessCore, stats, utils Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: 9f0b393cdd57ad288138cbe274e7d946 NeedsCompilation: no Package: FScanR Version: 1.8.0 Depends: R (>= 4.0) Imports: stats Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 9eea5e3aea089f3e89d9ac5e18687515 NeedsCompilation: no Package: FunChIP Version: 1.24.0 Depends: R (>= 3.5.0), GenomicRanges Imports: shiny, fda, doParallel, GenomicAlignments, Rcpp, methods, foreach, parallel, GenomeInfoDb, Rsamtools, grDevices, graphics, stats, RColorBrewer LinkingTo: Rcpp License: Artistic-2.0 MD5sum: 5640ba1fc069dd80849327c34befc7a6 NeedsCompilation: yes Package: funtooNorm Version: 1.22.0 Depends: R(>= 3.4) Imports: pls, matrixStats, minfi, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb, grDevices, graphics, stats Suggests: prettydoc, minfiData, knitr, rmarkdown License: GPL-3 MD5sum: d6e884ad73297602d50d66e42e48fdc4 NeedsCompilation: no Package: FuseSOM Version: 1.0.1 Depends: R (>= 4.2.0) Imports: psych, FCPS, analogue, coop, pheatmap, ggplotify, fastcluster, fpc, ggplot2, stringr, ggpubr, proxy, cluster, diptest, methods, SummarizedExperiment, stats, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, SingleCellExperiment License: GPL-2 MD5sum: 3d94408e2d1fc717ef6f306cbad315a6 NeedsCompilation: yes Package: GA4GHclient Version: 1.22.0 Depends: R (>= 3.5.0), S4Vectors Imports: BiocGenerics, Biostrings, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, methods, VariantAnnotation Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: f8e2ccfee5a5ec4ef6d69c5672287881 NeedsCompilation: no Package: GA4GHshiny Version: 1.20.0 Depends: GA4GHclient Imports: AnnotationDbi, BiocGenerics, dplyr, DT, GenomeInfoDb, openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny, shinyjs, tidyr, shinythemes Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 5accad4942c44d4dc89f807bd50e4126 NeedsCompilation: no Package: gaga Version: 2.44.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: parallel License: GPL (>= 2) MD5sum: 744126f64436444fccea8176eeef46ce NeedsCompilation: yes Package: gage Version: 2.48.0 Depends: R (>= 3.5.0) Imports: graph, KEGGREST, AnnotationDbi, GO.db Suggests: pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma License: GPL (>= 2.0) MD5sum: 9bce542740c670a1cd4f3ba1aa39fcd3 NeedsCompilation: no Package: gaggle Version: 1.66.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>= 0.4.17) License: GPL (>= 2) MD5sum: 57ff8d473c0af4d060e9a226d77cc20f NeedsCompilation: no Package: GAprediction Version: 1.24.0 Depends: R (>= 3.3) Imports: glmnet, stats, utils, Matrix Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 144a6462c2c70558a3225681fca826cf NeedsCompilation: no Package: garfield Version: 1.26.0 Suggests: knitr License: GPL-3 MD5sum: 43e981ca34ee93dc4a6a486189039b38 NeedsCompilation: yes Package: GARS Version: 1.18.0 Depends: R (>= 3.5), ggplot2, cluster Imports: DaMiRseq, MLSeq, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 06bec8c80aa90ef0e5a8fc0f34e47288 NeedsCompilation: no Package: GateFinder Version: 1.18.0 Imports: splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: a7706b6e4b17e8269c108b4d7db8c29e NeedsCompilation: no Package: GBScleanR Version: 1.2.14 Depends: SeqArray Imports: stats, utils, methods, ggplot2, tidyr, expm, Rcpp, RcppParallel, gdsfmt LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: a3bd0bcc1f10d16fa4fe4a27ff207a7c NeedsCompilation: yes Package: gcapc Version: 1.22.0 Depends: R (>= 3.4) Imports: BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings, BSgenome, GenomicRanges, Rsamtools, GenomicAlignments, matrixStats, MASS, splines, grDevices, graphics, stats, methods Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: GPL-3 MD5sum: d7ba08a1d100db010401a45ecda88e36 NeedsCompilation: no Package: gcatest Version: 1.28.2 Depends: R (>= 3.2) Imports: lfa Suggests: knitr, ggplot2 License: GPL-3 MD5sum: 083e1a76b08fec3b8718f34742ac2500 NeedsCompilation: yes Package: gCrisprTools Version: 2.4.0 Depends: R (>= 4.1) Imports: Biobase, limma, RobustRankAggreg, ggplot2, SummarizedExperiment, grid, rmarkdown, grDevices, graphics, methods, ComplexHeatmap, stats, utils, parallel Suggests: edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea License: Artistic-2.0 MD5sum: 8697be3504f496933b4e2f178da1ceee NeedsCompilation: no Package: gcrma Version: 2.70.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector, Biostrings (>= 2.11.32), splines, BiocManager Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL MD5sum: 4bc61327d51b514dc215c47806573b02 NeedsCompilation: yes Package: GCSscore Version: 1.12.0 Depends: R (>= 3.6) Imports: BiocManager, Biobase, utils, methods, RSQLite, devtools, dplR, stringr, graphics, stats, affxparser, data.table Suggests: siggenes, GEOquery, R.utils License: GPL (>= 3) MD5sum: 37d9e78451873d8cee54f50c19b5a870 NeedsCompilation: no Package: GDCRNATools Version: 1.18.0 Depends: R (>= 3.5.0) Imports: shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel Suggests: knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: 9257806e6f0df44a9068f050cc1d029e NeedsCompilation: no Package: GDSArray Version: 1.18.0 Depends: R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>= 0.5.32) Imports: tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager License: GPL-3 MD5sum: e5b248144e7ee5496221dcf65cd814b8 NeedsCompilation: no Package: gdsfmt Version: 1.34.1 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics License: LGPL-3 MD5sum: d3ceaf3f2f7fce9efb1bbef756fcf266 NeedsCompilation: yes Package: GEM Version: 1.24.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown License: Artistic-2.0 MD5sum: 0c0c434a859ef5f1c4375d70877769c1 NeedsCompilation: no Package: gemini Version: 1.12.0 Depends: R (>= 4.1.0) Imports: dplyr, grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: b6f766f7f6b868d4e3dd6f362f64107a NeedsCompilation: no Package: gemma.R Version: 1.0.1 Imports: magrittr, glue, memoise, jsonlite, data.table, rlang, lubridate, utils, stringr, SummarizedExperiment, Biobase, tibble, tidyr, S4Vectors, httr, rappdirs, bit64 Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis License: Apache License (>= 2) MD5sum: b9a86a8899a38d7520457cc7a1364b56 NeedsCompilation: no Package: genArise Version: 1.74.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: 29a1d26d9b9b8bd343c1963ab4eee375 NeedsCompilation: no Package: genbankr Version: 1.26.0 Depends: methods Imports: BiocGenerics, IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), GenomicFeatures (>= 1.31.5), Biostrings, VariantAnnotation, rtracklayer, S4Vectors (>= 0.17.28), GenomeInfoDb, Biobase Suggests: RUnit, rentrez, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 4c04bddf5b5c6319eabb8c00791264f5 NeedsCompilation: no Package: GeneAccord Version: 1.15.0 Depends: R (>= 3.5) Imports: biomaRt, caTools, dplyr, ggplot2, graphics, grDevices, gtools, ggpubr, magrittr, maxLik, RColorBrewer, reshape2, stats, tibble, utils Suggests: assertthat, BiocStyle, devtools, knitr, rmarkdown, testthat License: file LICENSE MD5sum: 8e2378e682a98ec7d5c648050f604311 NeedsCompilation: no Package: geneAttribution Version: 1.24.0 Imports: utils, GenomicRanges, org.Hs.eg.db, BiocGenerics, GenomeInfoDb, GenomicFeatures, IRanges, rtracklayer Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 544924665a025512a7fbae129df9d66f NeedsCompilation: no Package: GeneBreak Version: 1.28.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: df0c2a7e2f64835fe2b31854fe4ee0ad NeedsCompilation: no Package: geneClassifiers Version: 1.22.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: 0bc02f7d57cde6260f35b8ab32288ed4 NeedsCompilation: no Package: GeneExpressionSignature Version: 1.44.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: f2097f153018d759d0c48b8f43dca38b NeedsCompilation: no Package: genefilter Version: 1.80.3 Imports: BiocGenerics, AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 MD5sum: edad8d6bca4e69d60013613f26207b57 NeedsCompilation: yes Package: genefu Version: 2.30.0 Depends: R (>= 4.1), survcomp, biomaRt, iC10, AIMS Imports: amap, impute, mclust, limma, graphics, stats, utils Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown License: Artistic-2.0 MD5sum: a29769e87f67b3fd97a056560be7ad2a NeedsCompilation: no Package: GeneGA Version: 1.48.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: a986a9a8ddab49e94fc35817f32d5999 NeedsCompilation: no Package: GeneGeneInteR Version: 1.24.0 Depends: R (>= 4.0) Imports: snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods License: GPL (>= 2) MD5sum: 400f2839067b6ee7b69f8b206c066b29 NeedsCompilation: yes Package: GeneMeta Version: 1.70.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: dbe85479610c82bc4799ad1a03cc4466 NeedsCompilation: no Package: GeneNetworkBuilder Version: 1.40.0 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db License: GPL (>= 2) MD5sum: 28db091e332b9bdbdea66e79fc955b9b NeedsCompilation: yes Package: GeneOverlap Version: 1.34.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 38427040d6c3d6da80207f4da1f3eb6a NeedsCompilation: no Package: geneplast Version: 1.24.1 Depends: R (>= 4.0), methods Imports: igraph, snow, ape, grDevices, graphics, stats, utils, data.table Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: f27519844bf64ec209ba15fa0258e316 NeedsCompilation: no Package: geneplotter Version: 1.76.0 Depends: R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate Imports: AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db License: Artistic-2.0 MD5sum: 16c5a8f55d43a3dba0ac29eb801f7c29 NeedsCompilation: no Package: geneRecommender Version: 1.70.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: aac6ea09d3cce05f9e9a0058d3eb70bc NeedsCompilation: no Package: GeneRegionScan Version: 1.54.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) MD5sum: 81798867dd3ee484d8a9590a7ba2d3b6 NeedsCompilation: no Package: geneRxCluster Version: 1.34.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: cf994ae3d7dc824451f4576d3a9dd47b NeedsCompilation: yes Package: GeneSelectMMD Version: 2.42.3 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: a0cc2dd1b9d94f309ccfcf285e21d467 NeedsCompilation: yes Package: GENESIS Version: 2.28.0 Imports: Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 56e24fb6f32d4c9f102b3074ce86d881 NeedsCompilation: yes Package: GeneStructureTools Version: 1.18.0 Imports: Biostrings,GenomicRanges,IRanges,data.table,plyr,stringdist,stringr,S4Vectors,BSgenome.Mmusculus.UCSC.mm10,stats,utils,Gviz,rtracklayer,methods Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 393e92d07cffc45540c7eb4bf21236bf NeedsCompilation: no Package: geNetClassifier Version: 1.38.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics, grDevices Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) MD5sum: 4a54f89f055a14e6bd4341193b83eb8f NeedsCompilation: no Package: GeneticsPed Version: 1.60.3 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: 4c13272db974ffa612f1b91bc06e5750 NeedsCompilation: yes Package: GeneTonic Version: 2.2.0 Depends: R (>= 4.0.0) Imports: AnnotationDbi, backbone, bs4Dash (>= 2.0.0), circlize, colorspace, colourpicker, ComplexHeatmap, ComplexUpset, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce, ggplot2, ggrepel, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinyAce, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tippy, tools, utils, viridis, visNetwork Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: b99284baf334861c911daa3b77492abb NeedsCompilation: no Package: geneXtendeR Version: 1.24.0 Depends: rtracklayer, GO.db, R (>= 3.5.0) Imports: data.table, dplyr, graphics, networkD3, RColorBrewer, SnowballC, tm, utils, wordcloud, AnnotationDbi, BiocStyle, org.Rn.eg.db Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer License: GPL (>= 3) MD5sum: 4bcfa9e2d7121949ad609e6dd95ccc4d NeedsCompilation: yes Package: GENIE3 Version: 1.20.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods License: GPL (>= 2) MD5sum: 4e7d20a2312519ef7a4270f7c57afd5b NeedsCompilation: yes Package: genoCN Version: 1.50.0 Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: 4c53f4efeea51711c6658d1e7048bf5c NeedsCompilation: yes Package: genomation Version: 1.30.0 Depends: R (>= 3.5.0), grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 173e543aae963b1c5276666aca99cb21 NeedsCompilation: yes Package: GenomAutomorphism Version: 1.0.3 Depends: R (>= 4.2), Imports: Biostrings, BiocGenerics, BiocParallel, GenomeInfoDb, GenomicRanges, IRanges, dplyr, data.table, parallel, doParallel, foreach, methods, S4Vectors, stats, numbers, utils Suggests: spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr License: Artistic-2.0 MD5sum: b0fbf5f38939ecf0d5667eda6a51652e NeedsCompilation: no Package: GenomeInfoDb Version: 1.34.9 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.25.12), IRanges (>= 2.13.12) Imports: stats, stats4, utils, RCurl, GenomeInfoDbData Suggests: GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 4f2943dd3daeeaddf33568a8b537d81f NeedsCompilation: no Package: genomeIntervals Version: 1.54.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 1.5.8), GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: b214c9e27721554808bc1c803d65f774 NeedsCompilation: no Package: genomes Version: 3.28.0 Depends: readr, curl License: GPL-3 MD5sum: bef2ad1de8e48861ba1a220736cf011c NeedsCompilation: no Package: GenomicAlignments Version: 1.34.1 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.55.7), Rsamtools (>= 1.31.2) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 9f5b23e4f6b8658e47fac20d53beac4c NeedsCompilation: yes Package: GenomicDataCommons Version: 1.22.1 Depends: R (>= 3.4.0), magrittr Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, tibble Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table License: Artistic-2.0 MD5sum: aff70b1661d0b40190b65098726fb56e NeedsCompilation: no Package: GenomicDistributions Version: 1.6.0 Depends: R (>= 4.0), IRanges, GenomicRanges Imports: data.table, ggplot2, reshape2, methods, utils, Biostrings, plyr, dplyr, scales, broom, GenomeInfoDb, stats Suggests: AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData Enhances: BSgenome, extrafont, ensembldb, GenomicFeatures License: BSD_2_clause + file LICENSE MD5sum: 5c4e65e6fee3afa33a156c04ba0cbc68 NeedsCompilation: no Package: GenomicFeatures Version: 1.50.4 Depends: R (>= 3.5.0), BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29), IRanges (>= 2.13.23), GenomeInfoDb (>= 1.34.7), GenomicRanges (>= 1.31.17), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl, XVector (>= 0.19.7), Biostrings (>= 2.47.6), BiocIO, rtracklayer (>= 1.51.5), biomaRt (>= 2.17.1), Biobase (>= 2.15.1) Suggests: RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown License: Artistic-2.0 MD5sum: cc6e1d7ae0158fad765ad5fc59c21fe4 NeedsCompilation: no Package: GenomicFiles Version: 1.34.0 Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), MatrixGenerics, GenomicRanges (>= 1.31.16), SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3) Imports: GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25), VariantAnnotation (>= 1.27.9), GenomeInfoDb Suggests: BiocStyle, RUnit, genefilter, deepSNV, snpStats, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens License: Artistic-2.0 MD5sum: 03264fd9bf67d47d3e8844b3307affa5 NeedsCompilation: no Package: genomicInstability Version: 1.4.0 Depends: R (>= 4.1.0), checkmate Imports: mixtools, SummarizedExperiment Suggests: SingleCellExperiment, ExperimentHub, pROC License: file LICENSE MD5sum: e458921b9bc440fdef44d11d47c0cf88 NeedsCompilation: no Package: GenomicInteractionNodes Version: 1.2.0 Depends: R (>= 4.2.0), stats Imports: AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, GenomeInfoDb, methods, IRanges, RBGL, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: file LICENSE MD5sum: c04ed88fa81e9812f64d02cf9afa08ee NeedsCompilation: no Package: GenomicInteractions Version: 1.32.0 Depends: R (>= 3.5), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: d82d3a08381400e9abbc2f4ab849938a NeedsCompilation: no Package: GenomicOZone Version: 1.12.0 Depends: R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2 Imports: grDevices, stats, utils, plyr, gridExtra, lsr, parallel, ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack Suggests: readxl, GEOquery, knitr, rmarkdown License: LGPL (>= 3) MD5sum: db2908cde77a346513881dd5f3d46241 NeedsCompilation: no Package: GenomicRanges Version: 1.50.2 Depends: R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.31.2), GenomeInfoDb (>= 1.15.2) Imports: utils, stats, XVector (>= 0.29.2) LinkingTo: S4Vectors, IRanges Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: fbd8ce202a23da66d0df008f665ad74e NeedsCompilation: yes Package: GenomicScores Version: 2.10.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache, IRanges (>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub, rhdf5, DelayedArray, HDF5Array Suggests: RUnit, BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5, SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard License: Artistic-2.0 MD5sum: 8f72190f11c9a79e003c478c282e1b78 NeedsCompilation: no Package: GenomicSuperSignature Version: 1.6.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils License: Artistic-2.0 MD5sum: abeb255f416aa751f8bacc6665e7e390 NeedsCompilation: no Package: GenomicTuples Version: 1.32.0 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), GenomeInfoDb (>= 1.15.2), S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, covr License: Artistic-2.0 MD5sum: 421e3b71845113d4f878a85a2f86ddea NeedsCompilation: yes Package: genotypeeval Version: 1.30.0 Depends: R (>= 3.4.0), VariantAnnotation Imports: ggplot2, rtracklayer, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, methods, BiocParallel, graphics, stats Suggests: rmarkdown, testthat, SNPlocs.Hsapiens.dbSNP141.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: acfadf3133965dd89112f1204fc32b09 NeedsCompilation: no Package: GenProSeq Version: 1.2.0 Depends: keras, mclust, R (>= 4.2) Imports: tensorflow, word2vec, DeepPINCS, ttgsea, CatEncoders, reticulate, stats Suggests: knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: 567b4bf531054a988510d8e204f205c0 NeedsCompilation: no Package: GenVisR Version: 1.30.0 Depends: R (>= 3.3.0), methods Imports: AnnotationDbi, biomaRt (>= 2.45.8), BiocGenerics, Biostrings, DBI, GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, viridis, data.table, BSgenome, GenomeInfoDb, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 + file LICENSE MD5sum: 8724582b7c0d2dff1a18961ae8a3f587 NeedsCompilation: no Package: GeoDiff Version: 1.4.2 Depends: R (>= 4.1.0), Biobase Imports: Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods, graphics, stats, testthat, GeomxTools, NanoStringNCTools LinkingTo: Rcpp, RcppArmadillo, roptim Suggests: knitr, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: dc8e22bb2cfa0ba7c2e5850a90b0990c NeedsCompilation: yes Package: GEOexplorer Version: 1.4.0 Depends: shiny, limma, Biobase, plotly, shinyBS Imports: DT, htmltools, factoextra, heatmaply, maptools, pheatmap, scales, shinyHeatmaply, shinybusy, ggplot2, stringr, umap, GEOquery, impute, grDevices, stats, graphics, utils Suggests: rmarkdown, knitr, usethis, testthat (>= 3.0.0) License: GPL-3 MD5sum: 3cd384a467347c1eb15659190e903939 NeedsCompilation: no Package: GEOfastq Version: 1.6.0 Imports: xml2, rvest, stringr, RCurl, doParallel, foreach, plyr Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: e846523e38a1aab4b08338cd06a3af52 NeedsCompilation: no Package: GEOmetadb Version: 1.60.0 Depends: GEOquery,RSQLite Suggests: knitr, rmarkdown, dplyr, tm, wordcloud License: Artistic-2.0 MD5sum: 8559e4ea98e7a6a76de2af1fc9f17250 NeedsCompilation: no Package: GeomxTools Version: 3.2.0 Depends: R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors Imports: BiocGenerics, rjson, readxl, EnvStats, reshape2, methods, utils, stats, data.table, lmerTest, dplyr, stringr, grDevices, graphics, GGally, rlang, ggplot2, SeuratObject Suggests: rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork License: MIT MD5sum: cbfe2461c03f5e985f813a7fc41111e5 NeedsCompilation: no Package: GEOquery Version: 2.66.0 Depends: methods, Biobase Imports: readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr, limma, curl, R.utils Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr, markdown License: MIT MD5sum: 82a4255c26baa62569c2628133127c91 NeedsCompilation: no Package: GEOsubmission Version: 1.50.0 Imports: affy, Biobase, utils License: GPL (>= 2) MD5sum: a0334348ecfd798e129e9e3b6240d449 NeedsCompilation: no Package: gep2pep Version: 1.18.0 Imports: repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators Suggests: WriteXLS, testthat, knitr, rmarkdown License: GPL-3 MD5sum: c5a807db1b0564a83f6716447a5e3144 NeedsCompilation: no Package: gespeR Version: 1.30.0 Depends: methods, graphics, ggplot2, R(>= 2.10) Imports: Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel, parallel, foreach, reshape2, dplyr Suggests: knitr License: GPL-3 MD5sum: f642a7edb7753c6a5de25f1a1dc715f7 NeedsCompilation: no Package: getDEE2 Version: 1.8.0 Depends: R (>= 4.0) Imports: stats, utils, SummarizedExperiment, htm2txt Suggests: knitr, testthat, rmarkdown License: GPL-3 MD5sum: fc5f915e31ad3c70d8d709856812ecb4 NeedsCompilation: no Package: geva Version: 1.6.0 Depends: R (>= 4.1) Imports: grDevices, graphics, methods, stats, utils, dbscan, fastcluster, matrixStats Suggests: devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat (>= 3.0.0) License: LGPL-3 MD5sum: 0fd522e0a4162834ef540dfe0f27f124 NeedsCompilation: no Package: GEWIST Version: 1.42.0 Depends: R (>= 2.10), car License: GPL-2 MD5sum: edd7e6247133caf3efeb6803922a5ad7 NeedsCompilation: no Package: ggbio Version: 1.46.0 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.29.14), SummarizedExperiment, Biostrings, Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer (>= 1.25.16), GenomicFeatures (>= 1.29.11), OrganismDbi, GGally, ensembldb (>= 1.99.13), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: 5e79193a392e44b316a48971765cc65f NeedsCompilation: no Package: ggcyto Version: 1.26.4 Depends: methods, ggplot2(>= 3.3.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 3.33.1) Imports: plyr, scales, hexbin, data.table, RColorBrewer, gridExtra, rlang Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr License: file LICENSE MD5sum: efe65ac53a07caac9654cd73c674a8f6 NeedsCompilation: no Package: ggmanh Version: 1.2.0 Depends: methods, ggplot2 Imports: gdsfmt, ggrepel, grDevices, RColorBrewer, rlang, scales, SeqArray (>= 1.32.0), stats Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0), markdown, GenomicRanges License: MIT + file LICENSE MD5sum: 5074934ed49281781bcced61d8ec68b4 NeedsCompilation: no Package: ggmsa Version: 1.4.0 Depends: R (>= 4.1.0) Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot, RColorBrewer, ggalt, ggforce, dplyr, R4RNA, grDevices, seqmagick, grid, methods, statebins, ggtree (>= 1.17.1) Suggests: ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 4834345fed2f3deb95c4315693089506 NeedsCompilation: no Package: GGPA Version: 1.10.2 Depends: R (>= 4.0.0), stats, methods, graphics, GGally, network, sna, scales, matrixStats Imports: Rcpp (>= 0.11.3) LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle License: GPL (>= 2) MD5sum: 6e93368eebe9ad5288567a8f57bd6b92 NeedsCompilation: yes Package: ggspavis Version: 1.4.0 Depends: ggplot2 Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, methods, stats Suggests: BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 7e6273e3c7e5923662d01a5ae40727fd NeedsCompilation: no Package: ggtree Version: 3.6.2 Depends: R (>= 3.5.0) Imports: ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.0.6), yulab.utils, tidyr, tidytree (>= 0.3.9), treeio (>= 1.8.0), utils, scales, stats, cli Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue License: Artistic-2.0 MD5sum: 5a79326c18bd6ba525cfff8fdec991a2 NeedsCompilation: no Package: ggtreeDendro Version: 1.0.0 Depends: ggtree (>= 3.5.3) Imports: ggplot2, stats, tidytree Suggests: aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust, rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils License: Artistic-2.0 MD5sum: d3cf8188d0b7922c1ccb01f4e2b386d5 NeedsCompilation: no Package: ggtreeExtra Version: 1.8.1 Imports: ggplot2, utils, rlang, ggnewscale, stats, ggtree, tidytree (>= 0.3.9), cli Suggests: treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown, testthat (>= 3.0.0), pillar License: GPL (>= 3) MD5sum: 918e2c2cab73fb6c1df0574ee8ae1fcb NeedsCompilation: no Package: GIGSEA Version: 1.16.0 Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils Suggests: knitr, rmarkdown License: LGPL-3 MD5sum: 859ade235dfbc37d1c425dfc2af903d6 NeedsCompilation: no Package: girafe Version: 1.50.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), Rsamtools (>= 1.31.2), intervals (>= 0.13.1), ShortRead (>= 1.37.1), genomeIntervals (>= 1.25.1), grid Imports: methods, Biobase, Biostrings (>= 2.47.6), graphics, grDevices, stats, utils, IRanges (>= 2.13.12) Suggests: MASS, org.Mm.eg.db, RColorBrewer Enhances: genomeIntervals License: Artistic-2.0 MD5sum: d6002b60c4bfdfbc7d96d6b054399587 NeedsCompilation: yes Package: GISPA Version: 1.22.0 Depends: R (>= 3.5) Imports: Biobase, changepoint, data.table, genefilter, graphics, GSEABase, HH, lattice, latticeExtra, plyr, scatterplot3d, stats Suggests: knitr License: GPL-2 MD5sum: 2673bba202cbaddeae1ffaab1fc03c44 NeedsCompilation: no Package: GLAD Version: 2.62.0 Depends: R (>= 2.10) Imports: aws License: GPL-2 MD5sum: 7b90560d4c9ed3e1bb6875ac4c12d95d NeedsCompilation: yes Package: GladiaTOX Version: 1.14.0 Depends: R (>= 3.6.0), data.table (>= 1.9.4) Imports: DBI, RMySQL, RSQLite, numDeriv, RColorBrewer, parallel, stats, methods, graphics, grDevices, xtable, tools, brew, stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: b7fc6774f1ff8048cd714b6551b90fa8 NeedsCompilation: no Package: Glimma Version: 2.8.0 Depends: R (>= 4.0.0) Imports: htmlwidgets, edgeR, DESeq2, limma, SummarizedExperiment, stats, jsonlite, methods, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran License: GPL-3 MD5sum: 74140d23faf6a6fd0a7251a8a9ef5794 NeedsCompilation: no Package: glmGamPoi Version: 1.10.2 Imports: Rcpp, DelayedMatrixStats, matrixStats, MatrixGenerics, DelayedArray, HDF5Array, SummarizedExperiment, SingleCellExperiment, BiocGenerics, methods, stats, utils, splines, rlang LinkingTo: Rcpp, RcppArmadillo, beachmat Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, Matrix License: GPL-3 MD5sum: 5992b12b000d0b39b4f7cac0c19ad513 NeedsCompilation: yes Package: glmSparseNet Version: 1.16.0 Depends: R (>= 4.1), Matrix, MultiAssayExperiment, glmnet Imports: SummarizedExperiment, biomaRt, futile.logger, futile.options, forcats, utils, dplyr, glue, readr, digest, httr, ggplot2, survminer, reshape2, stringr, parallel, methods Suggests: testthat, knitr, rmarkdown, survival, survcomp, pROC, VennDiagram, BiocStyle, curatedTCGAData, TCGAutils License: GPL-3 MD5sum: 00af606f3239fb05105c60a29c736378 NeedsCompilation: no Package: GlobalAncova Version: 4.16.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: dd4a24f2b8ab82cf1ff28999218b1066 NeedsCompilation: yes Package: globalSeq Version: 1.26.0 Depends: R (>= 3.0.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 MD5sum: b6809aaf41e720ad6e3b0fcaaa8f8d20 NeedsCompilation: no Package: globaltest Version: 5.52.1 Depends: methods, survival Imports: Biobase, AnnotationDbi, annotate, graphics Suggests: vsn, golubEsets, KEGGREST, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart, mstate License: GPL (>= 2) MD5sum: 2573a81dd323c36f70a1015e997b97d9 NeedsCompilation: no Package: gmapR Version: 1.40.0 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2) Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome, GenomicAlignments (>= 1.15.6), BiocParallel Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines License: Artistic-2.0 MD5sum: 5a9fabd1b591f665b77a2b69a3565e80 NeedsCompilation: yes Package: GmicR Version: 1.12.0 Imports: AnnotationDbi, ape, bnlearn, Category, DT, doParallel, foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db, org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics, reshape2, stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 + file LICENSE MD5sum: c585e49d51b3c37b07f968244ea1196f NeedsCompilation: no Package: gmoviz Version: 1.10.0 Depends: circlize, GenomicRanges, graphics, R (>= 4.0) Imports: grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics, Biostrings, GenomeInfoDb, methods, GenomicAlignments, GenomicFeatures, IRanges, rtracklayer, pracma, colorspace, S4Vectors Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager License: GPL-3 MD5sum: e1474f1530946f92ba8b73e31411ab47 NeedsCompilation: no Package: GMRP Version: 1.26.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: a063013e66049ad6996189ea2592b975 NeedsCompilation: no Package: GNET2 Version: 1.14.0 Depends: R (>= 3.6) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment,dplyr,igraph, grDevices, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 MD5sum: 49a12c45df8be6aa099e18f6d859c09b NeedsCompilation: yes Package: GOexpress Version: 1.32.0 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), randomForest (>= 4.6), RCurl (>= 1.95) Suggests: BiocStyle License: GPL (>= 3) MD5sum: cfb6ee0bc0be19c2b1c6a7e51a735cd8 NeedsCompilation: no Package: GOfuncR Version: 1.18.0 Depends: R (>= 3.4), vioplot (>= 0.2), Imports: Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils, grDevices, graphics, stats, LinkingTo: Rcpp Suggests: Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat License: GPL (>= 2) MD5sum: 4157c08d56c092708fa72cc03af904eb NeedsCompilation: yes Package: GOpro Version: 1.24.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, dendextend, doParallel, foreach, parallel, org.Hs.eg.db, GO.db, Rcpp, stats, graphics, MultiAssayExperiment, IRanges, S4Vectors LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat License: GPL-3 MD5sum: 2fdea8165698e37c4b45bca4d8b236c3 NeedsCompilation: yes Package: goProfiles Version: 1.60.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: 05307b9d9a21a158178dfe30101b286a NeedsCompilation: no Package: GOSemSim Version: 2.24.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, GO.db, methods, utils LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat, ROCR License: Artistic-2.0 MD5sum: 3c42cebf69b137c02f1e8044ba2d51d3 NeedsCompilation: yes Package: goseq Version: 1.50.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2) Imports: mgcv, graphics, stats, utils, AnnotationDbi, GO.db,BiocGenerics Suggests: edgeR, org.Hs.eg.db, rtracklayer License: LGPL (>= 2) MD5sum: 523dc7a0592832e5f6f757ce4e6b95af NeedsCompilation: no Package: GOSim Version: 1.36.0 Depends: GO.db, annotate Imports: org.Hs.eg.db, AnnotationDbi, topGO, cluster, flexmix, RBGL, graph, Matrix, corpcor, Rcpp LinkingTo: Rcpp Enhances: igraph License: GPL (>= 2) MD5sum: fb033584663836b7922a42695c2f7782 NeedsCompilation: yes Package: goSorensen Version: 1.0.0 Depends: R (>= 4.2.0) Imports: GO.db, org.Hs.eg.db, goProfiles, stats, clusterProfiler, parallel Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: ebeeb3eb07dcb6cd28e1e19b0ae29a28 NeedsCompilation: no Package: goSTAG Version: 1.22.0 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 9380f7017563d69beefbbc5d3052c909 NeedsCompilation: no Package: GOstats Version: 2.64.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.43.2), graph Imports: methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 2d3d3bcf7a1465b915c7733b1df3edaa NeedsCompilation: no Package: GOsummaries Version: 2.34.0 Depends: R (>= 2.15), Rcpp Imports: plyr, grid, gProfileR, reshape2, limma, ggplot2, gtable LinkingTo: Rcpp Suggests: vegan License: GPL (>= 2) MD5sum: d9d36a04f95941465e0df3aae6765284 NeedsCompilation: yes Package: GOTHiC Version: 1.34.0 Depends: R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome, data.table Imports: BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils, stats, GenomeInfoDb Suggests: HiCDataLymphoblast Enhances: parallel License: GPL-3 MD5sum: dacdf9a96961f7380b9c7af6932655d3 NeedsCompilation: no Package: goTools Version: 1.72.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 MD5sum: 8f53950b070ae1b49661666205e4c8c9 NeedsCompilation: no Package: GPA Version: 1.10.0 Depends: R (>= 4.0.0), methods, graphics, Rcpp Imports: parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS, stats, utils, grDevices LinkingTo: Rcpp Suggests: gpaExample License: GPL (>= 2) MD5sum: 5b0def7c73be79ea5bb5471c4fb8a4f3 NeedsCompilation: yes Package: gpls Version: 1.70.0 Imports: stats Suggests: MASS License: Artistic-2.0 MD5sum: bf8637d55f183d264b86a57be6f13729 NeedsCompilation: no Package: gpuMagic Version: 1.14.0 Depends: R (>= 3.6.0), methods, utils Imports: Deriv, DescTools, digest, pryr, stringr, BiocGenerics LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 40a24b110193b39396861d94f94b5d21 NeedsCompilation: yes Package: GRaNIE Version: 1.2.7 Depends: R (>= 4.2.0) Imports: futile.logger, checkmate, patchwork, reshape2, data.table, matrixStats, Matrix, GenomicRanges, RColorBrewer, ComplexHeatmap, DESeq2, circlize, progress, utils, methods, stringr, scales, igraph, S4Vectors, ggplot2, rlang, Biostrings, GenomeInfoDb (>= 1.34.8), SummarizedExperiment, forcats, gridExtra, limma, tidyselect, readr, grid, tidyr, dplyr, stats, grDevices, graphics, magrittr, tibble, viridis, colorspace, biomaRt, topGO Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, IHW, clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, robust, variancePartition, purrr, EDASeq, JASPAR2022, TFBSTools, motifmatchr, rbioapi License: Artistic-2.0 MD5sum: f5276b64460bd269e4d9c912b25ae89c NeedsCompilation: no Package: granulator Version: 1.6.0 Depends: R (>= 4.1) Imports: cowplot, e1071, epiR, dplyr, dtangle, ggplot2, ggplotify, grDevices, limSolve, magrittr, MASS, nnls, parallel, pheatmap, purrr, rlang, stats, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 916a2ba21965ecadf34bf2bf63f7e669 NeedsCompilation: no Package: graper Version: 1.14.2 Depends: R (>= 3.6) Imports: Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: 531ef9c3c80e8114b7a43e804d7d831f NeedsCompilation: yes Package: graph Version: 1.76.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.11) Imports: stats, stats4, utils Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle, knitr Enhances: Rgraphviz License: Artistic-2.0 MD5sum: badc7573679f44bb44d3479b64634b83 NeedsCompilation: yes Package: GraphAlignment Version: 1.62.0 License: file LICENSE License_restricts_use: yes MD5sum: edb0f719d8f2d58aae054c8ebb35b568 NeedsCompilation: yes Package: GraphAT Version: 1.70.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL MD5sum: 67134f039471963a570c196759c77685 NeedsCompilation: no Package: graphite Version: 1.44.0 Depends: R (>= 4.2), methods Imports: AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats, utils, graphics, rlang, purrr Suggests: checkmate, a4Preproc, ALL, BiocStyle, clipper, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) License: AGPL-3 MD5sum: 499ad4b02115052f093d031b238a4e2d NeedsCompilation: no Package: GraphPAC Version: 1.40.0 Depends: R(>= 2.15),iPAC, igraph, TSP, RMallow Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 3cc8adbc18da456971fb3470940f4593 NeedsCompilation: no Package: GRENITS Version: 1.50.2 Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) Imports: graphics, grDevices, reshape2, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: network License: GPL (>= 2) MD5sum: 047e0d146c4ed25df4abc9b0add92b63 NeedsCompilation: yes Package: GreyListChIP Version: 1.30.0 Depends: R (>= 4.0), methods, GenomicRanges Imports: GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, RUnit Enhances: BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 640cf3caf4da1997b529d1f8c305379f NeedsCompilation: no Package: GRmetrics Version: 1.24.0 Depends: R (>= 4.0), SummarizedExperiment Imports: drc, plotly, ggplot2, S4Vectors, stats Suggests: knitr, rmarkdown, BiocStyle, tinytex License: GPL-3 MD5sum: 485f0c5163a6ad7414e9a4f6d4bc8525 NeedsCompilation: no Package: groHMM Version: 1.32.0 Depends: R (>= 3.0.2), MASS, parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), rtracklayer (>= 1.39.7) Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 6ad4aecd0511dc9a0069c808c58e6537 NeedsCompilation: yes Package: GRridge Version: 1.22.0 Depends: R (>= 3.2), penalized, Iso, survival, methods, graph,stats,glmnet,mvtnorm Suggests: testthat License: GPL-3 MD5sum: 5c7da0baf7039c0cf766a9b0f904c1dd NeedsCompilation: no Package: GSALightning Version: 1.26.0 Depends: R (>= 3.3.0) Imports: Matrix, data.table, stats Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 82d44b6afdbb421deb7fc964a8a9f7c2 NeedsCompilation: no Package: GSAR Version: 1.32.1 Depends: R (>= 3.0.1), igraph (>= 0.7.1) Imports: stats, graphics Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle License: GPL (>= 2) MD5sum: 20d4111a82f5fd4148a9feffaf5466d9 NeedsCompilation: no Package: GSCA Version: 2.28.0 Depends: shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5, R(>= 2.10.0) Imports: graphics Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr License: GPL (>= 2) MD5sum: b19c1d96f36147bc811bfa32a5cf1e52 NeedsCompilation: no Package: gscreend Version: 1.12.0 Depends: R (>= 3.6) Imports: SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics Suggests: knitr, testthat, rmarkdown License: GPL-3 MD5sum: 6cd53dbce19a2b7fa90a8723b0016ed0 NeedsCompilation: no Package: GSEABase Version: 1.60.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.13.8), Biobase (>= 2.17.8), annotate (>= 1.45.3), methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: 3464e4b41ae5e874ac3578b7c275d0c0 NeedsCompilation: no Package: GSEABenchmarkeR Version: 1.18.0 Depends: R (>= 3.5.0), Biobase, SummarizedExperiment Imports: AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, S4Vectors, stats, utils Suggests: BiocStyle, GSE62944, knitr, rappdirs, rmarkdown License: Artistic-2.0 MD5sum: 70aa75c38e377ede213765cd3b985a08 NeedsCompilation: no Package: GSEAlm Version: 1.58.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: 60a03344159b6cea974b408dec1f9e99 NeedsCompilation: no Package: GSEAmining Version: 1.8.0 Depends: R (>= 4.0) Imports: dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud, stringr, gridExtra, rlang, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat License: GPL-3 | file LICENSE MD5sum: ee6f82ee0e4ba8a6adf3bd8c2b676c5d NeedsCompilation: no Package: gsean Version: 1.18.0 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, knitr, plotly, WGCNA, rmarkdown License: Artistic-2.0 MD5sum: af8351484ad5740f79512f70044db092 NeedsCompilation: yes Package: GSgalgoR Version: 1.8.0 Imports: cluster, doParallel, foreach, matchingR, nsga2R, survival, proxy, stats, methods, Suggests: knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp, Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP, iC10TrainingData, pamr, testthat License: MIT + file LICENSE MD5sum: 8a92531fef208ec8cca196ecb84545a1 NeedsCompilation: no Package: GSReg Version: 1.32.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi Suggests: GenomicRanges, GSBenchMark License: GPL-2 MD5sum: 4a0727064122a022a0d56f314a4bcaa2 NeedsCompilation: yes Package: GSRI Version: 2.46.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 MD5sum: cf0a827380ef6694c68a9baa7d224255 NeedsCompilation: no Package: GSVA Version: 1.46.0 Depends: R (>= 3.5.0) Imports: methods, stats, utils, graphics, S4Vectors, IRanges, Biobase, SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel, BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray, DelayedMatrixStats, HDF5Array, BiocSingular Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinydashboard, ggplot2, data.table, plotly, future, promises, shinybusy, shinyjs License: GPL (>= 2) MD5sum: 696e724a9f07dd1204581bf1dbd0d26e NeedsCompilation: yes Package: gtrellis Version: 1.30.0 Depends: R (>= 3.1.2), grid, IRanges, GenomicRanges Imports: circlize (>= 0.4.8), GetoptLong, grDevices, utils Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff License: MIT + file LICENSE MD5sum: a36dfe004d7761b4375c661f75417a42 NeedsCompilation: no Package: GUIDEseq Version: 1.28.0 Depends: R (>= 3.5.0), GenomicRanges, BiocGenerics Imports: Biostrings, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma,dplyr, GenomicFeatures, rio, tidyr, tools, methods, purrr, ggplot2, openxlsx, patchwork, rlang Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: a3d2591b32fc8388d12b51d36c20d742 NeedsCompilation: no Package: Guitar Version: 2.14.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges, magrittr, ggplot2, methods, stats,utils ,knitr,dplyr License: GPL-2 MD5sum: 411da76451fe16597a333022f2ad498e NeedsCompilation: no Package: Gviz Version: 1.42.1 Depends: R (>= 4.2), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.17.20), grid Imports: XVector (>= 0.5.7), rtracklayer (>= 1.25.13), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.17.22), ensembldb (>= 2.11.3), BSgenome (>= 1.33.1), Biostrings (>= 2.33.11), biovizBase (>= 1.13.8), Rsamtools (>= 1.17.28), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>= 1.1.16), GenomeInfoDb (>= 1.1.3), BiocGenerics (>= 0.11.3), digest(>= 0.6.8), graphics, grDevices, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 202e768610e065f9e0768e4242fcc2cb NeedsCompilation: no Package: GWAS.BAYES Version: 1.8.0 Depends: R (>= 4.0), Rcpp (>= 1.0.3), RcppEigen (>= 0.3.3.7.0), GA (>= 3.2), caret (>= 6.0-86), ggplot2 (>= 3.3.0), doParallel (>= 1.0.15), memoise (>= 1.1.0), reshape2 (>= 1.4.4), Matrix (>= 1.2-18) LinkingTo: RcppEigen (>= 0.3.3.7.0),Rcpp (>= 1.0.3) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP, qqman License: GPL-2 | GPL-3 MD5sum: 7ee51b78011386e07acf41c05ce646a4 NeedsCompilation: yes Package: gwascat Version: 2.30.0 Depends: R (>= 3.5.0), methods Imports: S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges (>= 1.29.6), GenomicFeatures, readr, Biostrings, AnnotationDbi, BiocFileCache, snpStats, VariantAnnotation, AnnotationHub Suggests: DO.db, DT, knitr, RBGL, testthat, rmarkdown, dplyr, Gviz, Rsamtools, rtracklayer, graph, ggbio, DelayedArray, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BiocStyle Enhances: SNPlocs.Hsapiens.dbSNP144.GRCh37 License: Artistic-2.0 MD5sum: 6d61c527d10782f43d4e6f988bda593e NeedsCompilation: no Package: GWASTools Version: 1.44.0 Depends: Biobase Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel License: Artistic-2.0 MD5sum: d631af418a3325e06129f4851da3ca9a NeedsCompilation: no Package: gwasurvivr Version: 1.16.0 Depends: R (>= 3.4.0) Imports: GWASTools, survival, VariantAnnotation, parallel, matrixStats, SummarizedExperiment, stats, utils, SNPRelate Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 048a4ddf00bd11725a335df2cdbcf173 NeedsCompilation: no Package: GWENA Version: 1.8.0 Depends: R (>= 4.1) Imports: WGCNA (>= 1.67), dplyr (>= 0.8.3), dynamicTreeCut (>= 1.63-1), ggplot2 (>= 3.1.1), gprofiler2 (>= 0.1.6), magrittr (>= 1.5), tibble (>= 2.1.1), tidyr (>= 1.0.0), NetRep (>= 1.2.1), igraph (>= 1.2.4.1), RColorBrewer (>= 1.1-2), purrr (>= 0.3.3), rlist (>= 0.4.6.1), matrixStats (>= 0.55.0), SummarizedExperiment (>= 1.14.1), stringr (>= 1.4.0), cluster (>= 2.1.0), grDevices (>= 4.0.4), methods, graphics, stats, utils Suggests: testthat (>= 2.1.0), knitr (>= 1.25), rmarkdown (>= 1.16), prettydoc (>= 0.3.0), httr (>= 1.4.1), S4Vectors (>= 0.22.1), BiocStyle (>= 2.15.8) License: GPL-3 MD5sum: 8ab9a7f3b0a079c97b8061c02af15216 NeedsCompilation: no Package: h5vc Version: 2.32.0 Depends: grid, gridExtra, ggplot2 Imports: rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>= 2.13.1), methods, GenomicRanges, abind, BiocParallel, BatchJobs, h5vcData, GenomeInfoDb LinkingTo: Rhtslib (>= 1.99.1) Suggests: knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown License: GPL (>= 3) MD5sum: 10d015ecdf344453eaafbe0326488ae9 NeedsCompilation: yes Package: hapFabia Version: 1.40.0 Depends: R (>= 3.6.0), Biobase, fabia (>= 2.3.1) Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: fc124056a638d8a5b30e968685db730b NeedsCompilation: yes Package: Harman Version: 1.26.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel, methods, matrixStats LinkingTo: Rcpp Suggests: HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva License: GPL-3 + file LICENCE MD5sum: 3ec4d88d55b80175e86c3c12773853ce NeedsCompilation: yes Package: Harshlight Version: 1.70.0 Depends: R (>= 2.10) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) MD5sum: 4fe7814f1f94baa36e407afa1fdfe559 NeedsCompilation: yes Package: hca Version: 1.6.0 Depends: R (>= 4.1) Imports: httr, jsonlite, dplyr, tibble, tidyr, readr, BiocFileCache, tools, utils, digest, shiny, miniUI, DT Suggests: LoomExperiment, SummarizedExperiment, SingleCellExperiment, S4Vectors, methods, testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 1e06854ef70c75472d67f9002a5731e7 NeedsCompilation: no Package: HDF5Array Version: 1.26.0 Depends: R (>= 3.4), methods, DelayedArray (>= 0.15.16), rhdf5 (>= 2.31.6) Imports: utils, stats, tools, Matrix, rhdf5filters, BiocGenerics (>= 0.31.5), S4Vectors, IRanges LinkingTo: S4Vectors (>= 0.27.13), Rhdf5lib Suggests: BiocParallel, GenomicRanges, SummarizedExperiment (>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, RUnit, SingleCellExperiment License: Artistic-2.0 MD5sum: fee08903ae4e10af009d8efce66f8df9 NeedsCompilation: yes Package: HDTD Version: 1.32.2 Depends: R (>= 4.1) Imports: stats, Rcpp (>= 1.0.1) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown License: GPL-3 MD5sum: ed48521770117aadd3331c010256b113 NeedsCompilation: yes Package: heatmaps Version: 1.22.0 Depends: R (>= 3.5.0) Imports: methods, grDevices, graphics, stats, Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage, RColorBrewer, BiocGenerics, GenomeInfoDb Suggests: BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 680cf9ae34857c5410121394ec01e3be NeedsCompilation: no Package: Heatplus Version: 3.6.0 Imports: graphics, grDevices, stats, RColorBrewer Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) MD5sum: 01c603979a9227a2ce481bb7e4e81296 NeedsCompilation: no Package: HelloRanges Version: 1.24.0 Depends: methods, BiocGenerics, S4Vectors (>= 0.17.39), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.10), Biostrings (>= 2.41.3), BSgenome, GenomicFeatures (>= 1.31.5), VariantAnnotation (>= 1.19.3), Rsamtools, GenomicAlignments (>= 1.15.7), rtracklayer (>= 1.33.8), GenomeInfoDb, SummarizedExperiment, BiocIO Imports: docopt, stats, tools, utils Suggests: HelloRangesData, BiocStyle License: GPL (>= 2) MD5sum: cffb7f1b83857131e5d804be315850c2 NeedsCompilation: no Package: HELP Version: 1.56.0 Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods License: GPL (>= 2) MD5sum: dd76775bf66ded83bc31d9fc481bd9c7 NeedsCompilation: no Package: HEM Version: 1.70.0 Depends: R (>= 2.1.0) Imports: Biobase, grDevices, stats, utils License: GPL (>= 2) MD5sum: abcb0d74441d558cb52b2f91b6ef0efa NeedsCompilation: yes Package: hermes Version: 1.2.0 Depends: ggfortify, R (>= 4.1), SummarizedExperiment (>= 1.16) Imports: assertthat, biomaRt, Biobase, BiocGenerics, checkmate (>= 2.1), circlize, ComplexHeatmap, DESeq2, dplyr, edgeR, EnvStats, forcats, GenomicRanges, ggplot2, ggrepel (>= 0.9), IRanges, lifecycle, limma, magrittr, matrixStats, methods, MultiAssayExperiment, purrr, R6, Rdpack, rlang, stats, S4Vectors, tidyr, utils Suggests: BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown, statmod, testthat (>= 2.0), vdiffr, withr License: Apache License 2.0 | file LICENSE MD5sum: 0372b41dcaaeab8e37c2b3bd22c4b42a NeedsCompilation: no Package: Herper Version: 1.8.1 Depends: R (>= 4.0), reticulate Imports: utils, rjson, withr, stats Suggests: BiocStyle, testthat, knitr, rmarkdown, seqCNA License: GPL-3 MD5sum: df1308a4d08c4116fbafe996c0e77a63 NeedsCompilation: no Package: HGC Version: 1.6.0 Depends: R (>= 4.1.0) Imports: Rcpp (>= 1.0.0), RcppEigen(>= 0.3.2.0), Matrix, RANN, ape, dendextend, ggplot2, mclust, patchwork, dplyr, grDevices, methods, stats LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 2060f0b2d7abd9839cea6014ee8b81d1 NeedsCompilation: yes Package: hiAnnotator Version: 1.32.0 Depends: GenomicRanges, R (>= 2.10) Imports: foreach, iterators, rtracklayer, dplyr, BSgenome, ggplot2, scales, methods Suggests: knitr, doParallel, testthat, BiocGenerics, markdown License: GPL (>= 2) MD5sum: c3fbc36754fb405d62a9371fb6380777 NeedsCompilation: no Package: HIBAG Version: 1.34.1 Depends: R (>= 3.2.0) Imports: methods, RcppParallel LinkingTo: RcppParallel (>= 5.0.0) Suggests: parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr, markdown, rmarkdown License: GPL-3 MD5sum: 92c0fbdfb7aeaf551f2c63baea6cd21d NeedsCompilation: yes Package: HiCBricks Version: 1.16.0 Depends: R (>= 3.6), utils, curl, rhdf5, R6, grid Imports: ggplot2, viridis, RColorBrewer, scales, reshape2, stringr, data.table, GenomeInfoDb, GenomicRanges, stats, IRanges, grDevices, S4Vectors, digest, tibble, jsonlite, BiocParallel, R.utils, readr, methods Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 41d76d19ccfdd562e6836af0287ef3fb NeedsCompilation: no Package: HiCcompare Version: 1.20.0 Depends: R (>= 3.5.0), dplyr Imports: data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, QDNAseq, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5 Suggests: knitr, rmarkdown, testthat, multiHiCcompare License: MIT + file LICENSE MD5sum: debebb27c908fb236b6da324f9ba4140 NeedsCompilation: no Package: HiCDCPlus Version: 1.6.0 Imports: Rcpp,InteractionSet,GenomicInteractions,bbmle,pscl,BSgenome,data.table,dplyr,tidyr,GenomeInfoDb,rlang,splines,MASS,GenomicRanges,IRanges,tibble,R.utils,Biostrings,rtracklayer,methods,S4Vectors LinkingTo: Rcpp Suggests: BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, RUnit, BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix, BiocFileCache, rappdirs Enhances: parallel License: GPL-3 MD5sum: 017a77de2affcfbf7a4aa16547c95aca NeedsCompilation: yes Package: HiCDOC Version: 1.0.0 Depends: InteractionSet, GenomicRanges, SummarizedExperiment, R (>= 4.1.0) Imports: methods, zlibbioc, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools, pbapply, BiocParallel, BiocGenerics, rhdf5, grid, ggpubr, gridExtra, ggExtra, data.table, multiHiCcompare, GenomeInfoDb LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager License: LGPL (>= 3) MD5sum: c84a415d83a6add2fb78aaa0bb4810d5 NeedsCompilation: yes Package: HiContacts Version: 1.0.0 Depends: R (>= 4.2) Imports: HiContactsData, InteractionSet, GenomicInteractions, GenomicRanges, IRanges, GenomeInfoDb, S4Vectors, BiocGenerics, methods, rhdf5, Matrix, vroom, tibble, tidyr, dplyr, glue, stringr, reticulate, ggplot2, ggrastr, scales Suggests: cowplot, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: a3069f9a5529217a4955ab7626fa4d27 NeedsCompilation: no Package: hierGWAS Version: 1.28.0 Depends: R (>= 3.2.0) Imports: fastcluster,glmnet, fmsb Suggests: BiocGenerics, RUnit, MASS License: GPL-3 MD5sum: 321facf0c58650dc44cd8f8fc90ee0e6 NeedsCompilation: no Package: hierinf Version: 1.16.0 Depends: R (>= 3.6.0) Imports: fmsb, glmnet, methods, parallel, stats Suggests: knitr, MASS, testthat License: GPL-3 | file LICENSE MD5sum: 17a4777e29c751cd0a1a20f80e42ba2e NeedsCompilation: no Package: HilbertCurve Version: 1.28.0 Depends: R (>= 3.6.0), grid Imports: methods, utils, HilbertVis, png, grDevices, circlize (>= 0.3.3), IRanges, GenomicRanges, polylabelr Suggests: knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0), markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown License: MIT + file LICENSE MD5sum: 59b6c5df11b45ff6735def4a27510c6f NeedsCompilation: no Package: HilbertVis Version: 1.56.0 Depends: R (>= 2.6.0), grid, lattice Suggests: IRanges, EBImage License: GPL (>= 3) MD5sum: 0ed88549e8392ed30c43e61ec54570c6 NeedsCompilation: yes Package: HilbertVisGUI Version: 1.56.0 Depends: R (>= 2.6.0), HilbertVis (>= 1.1.6) Suggests: lattice, IRanges License: GPL (>= 3) MD5sum: bf19ae216b55d12ba9fed073a2ffe6fa NeedsCompilation: yes Package: HiLDA Version: 1.12.0 Depends: R(>= 4.1), ggplot2 Imports: R2jags, abind, cowplot, grid, forcats, stringr, GenomicRanges, S4Vectors, XVector, Biostrings, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, BiocGenerics, tidyr, grDevices, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 01ba11900b8d1f792b7176ce88b9f8aa NeedsCompilation: yes Package: hipathia Version: 2.14.0 Depends: R (>= 3.6), igraph (>= 1.0.1), AnnotationHub(>= 2.6.5), MultiAssayExperiment(>= 1.4.9), SummarizedExperiment(>= 1.8.1) Imports: coin, stats, limma, grDevices, utils, graphics, preprocessCore, servr, DelayedArray, matrixStats, methods, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 50201a1eec92a1a35ccb8d95ac8b0785 NeedsCompilation: no Package: HIPPO Version: 1.10.0 Depends: R (>= 3.6.0) Imports: ggplot2, graphics, stats, reshape2, gridExtra, Rtsne, umap, dplyr, rlang, magrittr, irlba, Matrix, SingleCellExperiment, ggrepel Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 440881b568ba30fe6703bf4d3cad51d1 NeedsCompilation: no Package: hiReadsProcessor Version: 1.34.0 Depends: R (>= 3.5.0), Biostrings, GenomicAlignments, BiocParallel, hiAnnotator Imports: sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl, methods Suggests: knitr, testthat, markdown License: GPL-3 MD5sum: c45844b579da958016faa0e663008e83 NeedsCompilation: no Package: HIREewas Version: 1.16.0 Depends: R (>= 3.5.0) Imports: quadprog, gplots, grDevices, stats Suggests: BiocStyle, knitr, BiocGenerics License: GPL (>= 2) MD5sum: 6a4452795d33a86c8b9ad06eefa4fe33 NeedsCompilation: yes Package: HiTC Version: 1.42.0 Depends: R (>= 2.15.0), methods, IRanges, GenomicRanges Imports: Biostrings, graphics, grDevices, rtracklayer, RColorBrewer, Matrix, parallel, GenomeInfoDb Suggests: BiocStyle, HiCDataHumanIMR90 License: Artistic-2.0 MD5sum: f86018caf28a4ec792fc6caa3b45c224 NeedsCompilation: no Package: hmdbQuery Version: 1.18.0 Depends: R (>= 3.5), XML Imports: S4Vectors, methods, utils Suggests: knitr, annotate, gwascat, testthat, rmarkdown License: Artistic-2.0 MD5sum: dcaea8a5904329def19b35ea940b0cde NeedsCompilation: no Package: HMMcopy Version: 1.40.0 Depends: R (>= 2.10.0), data.table (>= 1.11.8) License: GPL-3 MD5sum: fd62e5a9b3780e0035d32338f47945be NeedsCompilation: yes Package: hopach Version: 2.58.0 Depends: R (>= 2.11.0), cluster, Biobase, methods Imports: graphics, grDevices, stats, utils, BiocGenerics License: GPL (>= 2) MD5sum: d2c7ce02853621fd1bc705c4e0bdd4b6 NeedsCompilation: yes Package: HPAanalyze Version: 1.16.0 Depends: R (>= 3.5.0) Imports: dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils, gridExtra Suggests: knitr, rmarkdown, markdown, devtools, BiocStyle License: GPL-3 + file LICENSE MD5sum: c7b7037d0905c6785ba4bf7afd0d6c5e NeedsCompilation: no Package: hpar Version: 1.40.0 Depends: R (>= 3.5.0) Imports: utils Suggests: org.Hs.eg.db, GO.db, knitr, BiocStyle, testthat, rmarkdown License: Artistic-2.0 MD5sum: 647bbfaf65eb2c67f1d185ef542f716c NeedsCompilation: no Package: HPAStainR Version: 1.8.0 Depends: R (>= 4.1.0), dplyr, tidyr Imports: utils, stats, scales, stringr, tibble, shiny, data.table Suggests: knitr, BiocManager, qpdf, hpar, testthat, rmarkdown License: Artistic-2.0 MD5sum: 85c3f50819fed8bce11ac343a6047601 NeedsCompilation: no Package: HPiP Version: 1.4.3 Depends: R (>= 4.1) Imports: dplyr (>= 1.0.6), httr (>= 1.4.2), readr, tidyr, tibble, utils, stringr, magrittr, caret, corrplot, ggplot2, pROC, PRROC, igraph, graphics, stats, purrr, grDevices, protr, MCL Suggests: rmarkdown, colorspace, e1071, kernlab, ranger, SummarizedExperiment, Biostrings, randomForest, gprofiler2, gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools, knitr License: MIT + file LICENSE MD5sum: cb99c65d64a5ae07de9c9f5e8b60d082 NeedsCompilation: no Package: HTqPCR Version: 1.52.0 Depends: Biobase, RColorBrewer, limma Imports: affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils Suggests: statmod License: Artistic-2.0 MD5sum: 429523d4a681c7f29347d1c4680f201c NeedsCompilation: no Package: HTSeqGenie Version: 4.28.1 Depends: R (>= 3.5.0), gmapR (>= 1.8.0), ShortRead (>= 1.19.13), VariantAnnotation (>= 1.8.3) Imports: BiocGenerics (>= 0.2.0), S4Vectors (>= 0.9.25), IRanges (>= 1.21.39), GenomicRanges (>= 1.23.21), Rsamtools (>= 1.8.5), Biostrings (>= 2.24.1), chipseq (>= 1.6.1), hwriter (>= 1.3.0), Cairo (>= 1.5.5), GenomicFeatures (>= 1.9.31), BiocParallel, parallel, tools, rtracklayer (>= 1.17.19), GenomicAlignments, VariantTools (>= 1.7.7), GenomeInfoDb, SummarizedExperiment, methods Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, LungCancerLines, org.Hs.eg.db License: Artistic-2.0 MD5sum: e6363af0033ee063e1abb63a481c0082 NeedsCompilation: no Package: HTSFilter Version: 1.38.0 Depends: R (>= 4.0.0) Imports: edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices, graphics, methods Suggests: EDASeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: b2c78f385bd578d77004db56b2cee715 NeedsCompilation: no Package: HubPub Version: 1.6.0 Imports: available, usethis, biocthis, dplyr, aws.s3, fs, BiocManager, utils Suggests: AnnotationHubData, ExperimentHubData, testthat, knitr, rmarkdown, BiocStyle, License: Artistic-2.0 MD5sum: f996aed5ee39abacca57b821fe1e49dd NeedsCompilation: no Package: HumanTranscriptomeCompendium Version: 1.14.0 Depends: R (>= 3.6) Imports: shiny, ssrch, S4Vectors, SummarizedExperiment, utils Suggests: knitr, BiocStyle, beeswarm, tximportData, DT, tximport, dplyr, magrittr, BiocFileCache, testthat, rhdf5client, rmarkdown License: Artistic-2.0 MD5sum: 4a8495aa25207670ee958c978758ba66 NeedsCompilation: no Package: hummingbird Version: 1.8.0 Depends: R (>= 4.0) Imports: Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges LinkingTo: Rcpp Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 4b1b40926e9cff88e4850cd0c1975e4f NeedsCompilation: yes Package: HybridMTest Version: 1.42.0 Depends: R (>= 2.9.0), Biobase, fdrtool, MASS, survival Imports: stats License: GPL (>= 2) MD5sum: 6fec564c3b2aace09ab2d284b0717ff6 NeedsCompilation: no Package: hypeR Version: 1.14.0 Depends: R (>= 3.6.0) Imports: ggplot2, ggforce, R6, magrittr, dplyr, purrr, stats, stringr, scales, rlang, httr, openxlsx, htmltools, reshape2, reactable, msigdbr, kableExtra, rmarkdown, igraph, visNetwork, shiny Suggests: tidyverse, devtools, testthat, knitr License: GPL-3 + file LICENSE MD5sum: 4121a78b4bf75afdd01b761be0f2be1a NeedsCompilation: no Package: hyperdraw Version: 1.50.0 Depends: R (>= 2.9.0) Imports: methods, grid, graph, hypergraph, Rgraphviz, stats4 License: GPL (>= 2) MD5sum: 086dc68fc216e4df6df9d02bf0a671f5 NeedsCompilation: no Package: hypergraph Version: 1.70.0 Depends: R (>= 2.1.0), methods, utils, graph Suggests: BiocGenerics, RUnit License: Artistic-2.0 MD5sum: fc5ed8a8b82b888e5095eaadeeb4248a NeedsCompilation: no Package: iASeq Version: 1.42.0 Depends: R (>= 2.14.1) Imports: graphics, grDevices License: GPL-2 MD5sum: 70c4ed4cbd87b48866ba38d354db6ef8 NeedsCompilation: no Package: iasva Version: 1.16.0 Depends: R (>= 3.5), Imports: irlba, stats, cluster, graphics, SummarizedExperiment, BiocParallel Suggests: knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot, DescTools, RColorBrewer License: GPL-2 MD5sum: 4e7b70c5bb5336bb67be2e6f67d3c9c3 NeedsCompilation: no Package: iBBiG Version: 1.42.0 Depends: biclust Imports: stats4,xtable,ade4 Suggests: methods License: Artistic-2.0 MD5sum: 07d01bd3815117cde546ce8ef86a5bec NeedsCompilation: yes Package: ibh Version: 1.46.0 Depends: simpIntLists Suggests: yeastCC, stats License: GPL (>= 2) MD5sum: 0c3b54690c0d0286df8ccc842faea7ce NeedsCompilation: no Package: iBMQ Version: 1.38.0 Depends: R(>= 2.15.0),Biobase (>= 2.16.0), ggplot2 (>= 0.9.2) License: Artistic-2.0 MD5sum: a056821653db5459109fc3e172fb5ac9 NeedsCompilation: yes Package: iCARE Version: 1.26.0 Depends: R (>= 3.3.0), plotrix, gtools, Hmisc Suggests: RUnit, BiocGenerics License: GPL-3 + file LICENSE MD5sum: f3a3bfed9bde5598dc4d7a00d6789675 NeedsCompilation: yes Package: Icens Version: 1.70.0 Depends: survival Imports: graphics License: Artistic-2.0 MD5sum: 0cf1c275f889bcc3bc8d37e552144513 NeedsCompilation: no Package: icetea Version: 1.16.0 Depends: R (>= 4.0) Imports: stats, utils, methods, graphics, grDevices, ggplot2, GenomicFeatures, ShortRead, BiocParallel, Biostrings, S4Vectors, Rsamtools, BiocGenerics, IRanges, GenomicAlignments, GenomicRanges, rtracklayer, SummarizedExperiment, VariantAnnotation, limma, edgeR, csaw, DESeq2, TxDb.Dmelanogaster.UCSC.dm6.ensGene Suggests: knitr, rmarkdown, Rsubread (>= 1.29.0), testthat License: GPL-3 + file LICENSE MD5sum: d4d77e311de5bed6ac1c6f8f0e97be26 NeedsCompilation: no Package: iCheck Version: 1.28.0 Depends: R (>= 3.2.0), Biobase, lumi, gplots Imports: stats, graphics, preprocessCore, grDevices, randomForest, affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest, scatterplot3d, utils License: GPL (>= 2) MD5sum: 6109fae95ba18dde28e766750ad6f2cf NeedsCompilation: no Package: iChip Version: 1.52.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) MD5sum: 6b935119adc7fcfab78edc9a18efb0e5 NeedsCompilation: yes Package: iClusterPlus Version: 1.34.3 Depends: R (>= 3.3.0), parallel Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 446df9647ffb7593135e37ec7681d6ee NeedsCompilation: yes Package: iCNV Version: 1.18.0 Depends: R (>= 3.3.1), CODEX Imports: fields, ggplot2, truncnorm, tidyr, data.table, dplyr, grDevices, graphics, stats, utils, rlang Suggests: knitr, rmarkdown, WES.1KG.WUGSC License: GPL-2 MD5sum: f8cd3706a753d57d45c13c9afd7f1fba NeedsCompilation: no Package: iCOBRA Version: 1.26.0 Depends: R (>= 4.0) Imports: shiny (>= 0.9.1.9008), shinydashboard, shinyBS, reshape2, ggplot2 (>= 2.0.0), scales, ROCR, dplyr, DT, limma, methods, UpSetR, markdown Suggests: knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 855ad8f9d8bae650ca48651a6e224425 NeedsCompilation: no Package: ideal Version: 1.22.0 Depends: topGO Imports: DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0), heatmaply, plotly, pheatmap, pcaExplorer, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, DT, rentrez, rintrojs, rlang, ggrepel, knitr, rmarkdown, shinyAce, BiocParallel, grDevices, base64enc, methods Suggests: testthat, BiocStyle, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR License: MIT + file LICENSE MD5sum: 1eb9bcd77d4a94a823ba6db7631fa52f NeedsCompilation: no Package: IdeoViz Version: 1.34.0 Depends: R (>= 3.5.0), Biobase, IRanges, GenomicRanges, RColorBrewer, rtracklayer, graphics, GenomeInfoDb License: GPL-2 MD5sum: 3e95583d655f8d6d52936d698662ec56 NeedsCompilation: no Package: idiogram Version: 1.74.0 Depends: R (>= 2.10), methods, Biobase, annotate, plotrix Suggests: hu6800.db, hgu95av2.db, golubEsets License: GPL-2 MD5sum: 7d51b576734737dee8d48c0cf872e22c NeedsCompilation: no Package: idpr Version: 1.8.0 Depends: R (>= 4.1.0) Imports: ggplot2 (>= 3.3.0), magrittr (>= 1.5), dplyr (>= 0.8.5), plyr (>= 1.8.6), jsonlite (>= 1.6.1), rlang (>= 0.4.6), Biostrings (>= 2.56.0), methods (>= 4.0.0) Suggests: knitr, rmarkdown, msa, ape, testthat, seqinr License: LGPL (>= 3) MD5sum: 98d09f4004b057311727fe4ad89753c2 NeedsCompilation: no Package: idr2d Version: 1.12.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.6), futile.logger (>= 1.4.3), GenomeInfoDb (>= 1.14.0), GenomicRanges (>= 1.30), ggplot2 (>= 3.1.1), grDevices, grid, idr (>= 1.2), IRanges (>= 2.18.0), magrittr (>= 1.5), methods, reticulate (>= 1.13), scales (>= 1.0.0), stats, stringr (>= 1.3.1), utils Suggests: DT (>= 0.4), htmltools (>= 0.3.6), knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 111faa3f883d17b9de57ea471163f1a8 NeedsCompilation: no Package: iGC Version: 1.28.0 Depends: R (>= 3.2.0) Imports: plyr, data.table Suggests: BiocStyle, knitr, rmarkdown Enhances: doMC License: GPL-2 MD5sum: adc544778d006a630e94b1ab819d2148 NeedsCompilation: no Package: IgGeneUsage Version: 1.12.0 Depends: R (>= 4.2.0) Imports: methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0), SummarizedExperiment LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, gridExtra, ggrepel License: MIT + file LICENSE MD5sum: 0c9efbfe192d2309fa0ddad0e9892659 NeedsCompilation: yes Package: igvR Version: 1.18.1 Depends: R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz (>= 2.17.1) Imports: methods, BiocGenerics, httpuv, utils, rtracklayer, VariantAnnotation, RColorBrewer, httr Suggests: RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo License: MIT + file LICENSE MD5sum: c470f1474704efcfff03c9b843f904f6 NeedsCompilation: no Package: IHW Version: 1.26.0 Depends: R (>= 3.3.0) Imports: methods, slam, lpsymphony, fdrtool, BiocGenerics Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools License: Artistic-2.0 MD5sum: c8c7ad439df987dc6ae230cf7ed1059f NeedsCompilation: no Package: illuminaio Version: 0.40.0 Imports: base64 Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2), BiocStyle License: GPL-2 MD5sum: 09720bf90cecb5bdf6ce8a459e293341 NeedsCompilation: yes Package: ILoReg Version: 1.8.0 Depends: R (>= 4.0.0) Imports: Matrix, parallel, foreach, aricode, LiblineaR, SparseM, ggplot2, cowplot, RSpectra, umap, Rtsne, fastcluster, parallelDist, cluster, dendextend, DescTools, plyr, scales, pheatmap, reshape2, dplyr, doRNG, SingleCellExperiment, SummarizedExperiment, S4Vectors, methods, stats, doSNOW, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 31b0968a90c4489b5afcfee87035a6d4 NeedsCompilation: no Package: imageHTS Version: 1.48.0 Depends: R (>= 2.9.0), EBImage (>= 4.3.12), cellHTS2 (>= 2.10.0) Imports: tools, Biobase, hwriter, methods, vsn, stats, utils, e1071 Suggests: BiocStyle, MASS License: LGPL-2.1 MD5sum: 59a274d156e657c237e0ceaff50e0da9 NeedsCompilation: no Package: IMAS Version: 1.22.0 Depends: R (> 3.0.0),GenomicFeatures, ggplot2, IVAS Imports: doParallel, lme4, BiocGenerics, GenomicRanges, IRanges, foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, stats, ggfortify, grDevices, methods, Matrix, utils, graphics, gridExtra, grid, lattice, Rsamtools, survival, BiocParallel, GenomicAlignments, parallel Suggests: BiocStyle, RUnit License: GPL-2 MD5sum: da261c59ed59184de8982382a9a2a72b NeedsCompilation: no Package: imcRtools Version: 1.4.2 Depends: R (>= 4.1), SpatialExperiment Imports: S4Vectors, stats, utils, SummarizedExperiment, methods, pheatmap, scuttle, stringr, readr, EBImage, cytomapper, abind, BiocParallel, viridis, dplyr, magrittr, DT, igraph, SingleCellExperiment, vroom, BiocNeighbors, RTriangle, ggraph, tidygraph, ggplot2, data.table, sf, concaveman, tidyselect, distances, MatrixGenerics Suggests: CATALYST, grid, BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 MD5sum: dbaaa6bce7b568377e37d74fd92ae79d NeedsCompilation: no Package: IMMAN Version: 1.18.0 Imports: STRINGdb, Biostrings, igraph, graphics, utils, seqinr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: d37339ec4b7f34450fa6f1341d352482 NeedsCompilation: no Package: ImmuneSpaceR Version: 1.26.1 Depends: R (>= 3.5.0) Imports: utils, R6, data.table, curl, httr, Rlabkey (>= 2.3.1), Biobase, pheatmap, ggplot2 (>= 3.2.0), scales, stats, gplots, plotly, heatmaply (>= 0.7.0), jsonlite, rmarkdown, preprocessCore, flowCore, flowWorkspace, digest Suggests: knitr, testthat, covr, withr License: GPL-2 MD5sum: d092c8d110782396dd73cc05243f5026 NeedsCompilation: no Package: immunoClust Version: 1.30.0 Depends: R(>= 3.6), flowCore Imports: methods, stats, graphics, grid, lattice, grDevices Suggests: BiocStyle, utils, testthat License: Artistic-2.0 MD5sum: af6686f550a3addb168fba5586b32265 NeedsCompilation: yes Package: immunotation Version: 1.5.0 Depends: R (>= 4.1) Imports: stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr, xml2, maps, rlang Suggests: BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT License: GPL-3 MD5sum: 6928e1ab1489d2c4dfa125038c86bdc8 NeedsCompilation: no Package: IMPCdata Version: 1.34.0 Depends: R (>= 2.3.0) Imports: rjson License: file LICENSE MD5sum: 5d0033583a1d7f2f45a027682244133f NeedsCompilation: no Package: impute Version: 1.72.3 Depends: R (>= 2.10) License: GPL-2 MD5sum: baa1f0961301290fe70dd79e274790cc NeedsCompilation: yes Package: INDEED Version: 2.12.0 Depends: glasso (>= 1.8), R (>= 3.5) Imports: devtools (>= 1.13.0), graphics (>= 3.3.1), stats (>= 3.3.1), utils (>= 3.3.1), igraph (>= 1.2.4), visNetwork(>= 2.0.6) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0) License: Artistic-2.0 MD5sum: 8b1f51b45f593dbc5aa278ace607d6dd NeedsCompilation: no Package: infercnv Version: 1.14.2 Depends: R(>= 4.0) Imports: graphics, grDevices, RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, phyclust, Matrix, fastcluster, parallelDist, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, digest, RANN, igraph, reshape2, rjags, fitdistrplus, future, foreach, doParallel, Seurat, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse Suggests: BiocStyle, knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: c7e0ea1ae020eb31ede9655c0634615a NeedsCompilation: no Package: infinityFlow Version: 1.8.0 Depends: R (>= 4.0.0), flowCore Imports: stats, grDevices, utils, graphics, pbapply, matlab, png, raster, grid, uwot, gtools, Biobase, generics, parallel, methods, xgboost Suggests: knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071 License: GPL-3 MD5sum: ca6052aa905a58bc1f4c810b7b0769f2 NeedsCompilation: no Package: Informeasure Version: 1.8.0 Depends: R (>= 4.0) Imports: entropy Suggests: knitr, rmarkdown, testthat, SummarizedExperiment License: GPL-3 MD5sum: e6e6b60623b78a76f05c5b748f48ace2 NeedsCompilation: no Package: InPAS Version: 2.6.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi,batchtools,Biobase,Biostrings,BSgenome,cleanUpdTSeq, depmixS4,dplyr,flock,future,future.apply,GenomeInfoDb,GenomicRanges, GenomicFeatures, ggplot2, IRanges, limma, magrittr,methods,parallelly, plyranges, preprocessCore, readr,reshape2, RSQLite, stats,S4Vectors, utils Suggests: BiocGenerics,BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, knitr, markdown, rmarkdown, rtracklayer, RUnit, grDevices, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL (>= 2) MD5sum: 0cb50ec2d6ad871617d663b318772bcb NeedsCompilation: no Package: INPower Version: 1.34.0 Depends: R (>= 3.1.0), mvtnorm Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE MD5sum: 028b8592df8fc63d4909754d9ff6bbd0 NeedsCompilation: no Package: INSPEcT Version: 1.28.0 Depends: R (>= 3.6), methods, Biobase, BiocParallel Imports: pROC, deSolve, rootSolve, KernSmooth, gdata, GenomicFeatures, GenomicRanges, IRanges, BiocGenerics, GenomicAlignments, Rsamtools, S4Vectors, GenomeInfoDb, DESeq2, plgem, rtracklayer, SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: fd76bc5656c0125fc89a25ffe65893b3 NeedsCompilation: no Package: InTAD Version: 1.18.0 Depends: R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges, MultiAssayExperiment, SummarizedExperiment,stats Imports: BiocGenerics,Biobase,rtracklayer,parallel,graphics,mclust,qvalue, ggplot2,utils,ggpubr Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 2c792fc59b1a96d7befa8a4a4274ef12 NeedsCompilation: no Package: intansv Version: 1.38.0 Depends: R (>= 2.14.0), plyr, ggbio, GenomicRanges Imports: BiocGenerics, IRanges License: MIT + file LICENSE MD5sum: d99a77be86cd36cba32a835c584a224c NeedsCompilation: no Package: interacCircos Version: 1.8.0 Depends: R (>= 4.1) Imports: RColorBrewer, htmlwidgets, plyr, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: b1bab11b02ff1f3cb0a217c13971c18d NeedsCompilation: no Package: InteractionSet Version: 1.26.1 Depends: GenomicRanges, SummarizedExperiment Imports: methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.27.12), IRanges, GenomeInfoDb LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 3717bbec61eaa705ad643ca30de03317 NeedsCompilation: yes Package: InteractiveComplexHeatmap Version: 1.6.0 Depends: R (>= 4.0.0), ComplexHeatmap (>= 2.11.0) Imports: grDevices, stats, shiny, grid, GetoptLong, S4Vectors (>= 0.26.1), digest, IRanges, kableExtra (>= 1.3.1), utils, svglite, htmltools, clisymbols, jsonlite, RColorBrewer, fontawesome Suggests: knitr, rmarkdown, testthat, EnrichedHeatmap, GenomicRanges, data.table, circlize, GenomicFeatures, tidyverse, tidyHeatmap, cluster, org.Hs.eg.db, simplifyEnrichment, GO.db, SC3, GOexpress, SingleCellExperiment, scater, gplots, pheatmap, airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve (>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks License: MIT + file LICENSE MD5sum: b133888faaefa74bd293705ee885dde8 NeedsCompilation: no Package: interactiveDisplay Version: 1.36.0 Depends: R (>= 3.5.0), methods, BiocGenerics, grid Imports: interactiveDisplayBase (>= 1.7.3), shiny, RColorBrewer, ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi Suggests: RUnit, hgu95av2.db, knitr, GenomicRanges, SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer, metagenomeSeq, gplots, vegan, Biobase Enhances: rstudio License: Artistic-2.0 MD5sum: fbedb786975f7b2801af9064bda55a1c NeedsCompilation: no Package: interactiveDisplayBase Version: 1.36.0 Depends: R (>= 2.10), methods, BiocGenerics Imports: shiny, DT Suggests: knitr, markdown Enhances: rstudioapi License: Artistic-2.0 MD5sum: 8e4b897fd6e3150c333d7fcf7e47710d NeedsCompilation: no Package: InterCellar Version: 2.4.0 Depends: R (>= 4.1) Imports: config, golem, shiny, DT, shinydashboard, shinyFiles, shinycssloaders, data.table, fs, dplyr, tidyr, circlize, colourpicker, dendextend, factoextra, ggplot2, plotly, plyr, shinyFeedback, shinyalert, tibble, umap, visNetwork, wordcloud2, readxl, htmlwidgets, colorspace, signal, scales, htmltools, ComplexHeatmap, grDevices, stats, tools, utils, biomaRt, rlang, fmsb, igraph Suggests: testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, httr License: MIT + file LICENSE MD5sum: f5726b7e9214c90c33089b6eeb5dec6a NeedsCompilation: no Package: IntEREst Version: 1.22.2 Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, SummarizedExperiment, edgeR, S4Vectors Imports: seqLogo, Biostrings, GenomicFeatures (>= 1.39.4), IRanges, seqinr, graphics, grDevices, stats, utils, grid, methods, DBI, RMySQL, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2 Suggests: clinfun, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-2 MD5sum: a787d32dada4fc5fccb10a90ce7e998d NeedsCompilation: no Package: InterMineR Version: 1.20.0 Depends: R (>= 3.4.1) Imports: Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, igraph, httr, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, methods Suggests: BiocStyle, Gviz, knitr, rmarkdown, GO.db, org.Hs.eg.db License: LGPL MD5sum: 87c23f38bcf693c73c1008fbd646ad3b NeedsCompilation: no Package: IntramiRExploreR Version: 1.20.0 Depends: R (>= 3.4) Imports: igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats, utils, grDevices, graphics Suggests: gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat License: GPL-2 MD5sum: fe7a435c3419bf8efaf6eaa12f344403 NeedsCompilation: no Package: IONiseR Version: 2.22.0 Depends: R (>= 3.4) Imports: rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2, methods, BiocGenerics, XVector, tibble, stats, BiocParallel, bit64, stringr, utils Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData License: MIT + file LICENSE MD5sum: 49239175d1845e21c822674b5627465b NeedsCompilation: no Package: iPAC Version: 1.42.0 Depends: R(>= 2.15),gdata, scatterplot3d, Biostrings, multtest License: GPL-2 MD5sum: e565549812ba9c1b2c83be4784d280c4 NeedsCompilation: no Package: iPath Version: 1.4.2 Depends: R (>= 4.1), mclust, BiocParallel, survival Imports: Rcpp (>= 1.0.5), matrixStats, ggpubr, ggplot2, survminer, stats LinkingTo: Rcpp, RcppArmadillo Suggests: rmarkdown, BiocStyle, knitr License: GPL-2 MD5sum: 5b62b57187bc027b6abaabcd7b74fe56 NeedsCompilation: yes Package: ipdDb Version: 1.16.0 Depends: R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1), AnnotationHub Imports: Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats, assertthat Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: c08642bd043f91cf7af2083633f63b11 NeedsCompilation: no Package: IPO Version: 1.24.0 Depends: xcms (>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats, utils Imports: BiocParallel Suggests: RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr Enhances: parallel License: GPL (>= 2) + file LICENSE MD5sum: a10fbd6f9bca925b3d6218a7af4851f1 NeedsCompilation: no Package: IRanges Version: 2.32.0 Depends: R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.39.2), S4Vectors (>= 0.33.3) Imports: stats4 LinkingTo: S4Vectors Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 4cace1518b529ce898b7e9f84fefa428 NeedsCompilation: yes Package: IRISFGM Version: 1.6.0 Depends: R (>= 4.1) Imports: Rcpp (>= 1.0.0), MCL, anocva, Polychrome, RColorBrewer, colorspace, AnnotationDbi, ggplot2, org.Hs.eg.db, org.Mm.eg.db, pheatmap, AdaptGauss, DEsingle,DrImpute, Matrix, Seurat, SingleCellExperiment, clusterProfiler, ggpubr, ggraph, igraph, mixtools, scater, scran, stats, methods, grDevices, graphics, utils, knitr LinkingTo: Rcpp Suggests: rmarkdown License: GPL-2 MD5sum: 36095c043bb604c283f4c51c3df5ac91 NeedsCompilation: yes Package: ISAnalytics Version: 1.8.3 Depends: R (>= 4.2) Imports: utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs, lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools, grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib, DT Suggests: testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown, roxygen2, vegan, withr, extraDistr, ggalluvial, scales, gridExtra, R.utils, RefManageR, flexdashboard, circlize, plotly, gtools, eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr, future, doFuture, foreach, psych, data.table, Rcapture License: CC BY 4.0 MD5sum: 5e8ad9a16d045331a84bbaba7c85e04d NeedsCompilation: no Package: iSEE Version: 2.10.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, ComplexHeatmap, circlize, grid Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools License: MIT + file LICENSE MD5sum: 546c5e997807b948d022c86d3c02bf87 NeedsCompilation: no Package: iSEEhex Version: 1.0.0 Depends: SummarizedExperiment, iSEE Imports: ggplot2, hexbin, methods, shiny Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), scRNAseq, scater License: Artistic-2.0 MD5sum: 15702faef4cdba4d1c99d6cfc2a3bea3 NeedsCompilation: no Package: iSEEhub Version: 1.0.0 Depends: SummarizedExperiment, SingleCellExperiment, ExperimentHub Imports: AnnotationHub, BiocManager, DT, iSEE, methods, rintrojs, S4Vectors, shiny, shinydashboard, shinyjs, utils Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), nullrangesData Enhances: BioPlex, biscuiteerData, bodymapRat, CLLmethylation, CopyNeutralIMA, curatedAdipoArray, curatedAdipoChIP, curatedMetagenomicData, curatedTCGAData, DMRcatedata, DuoClustering2018, easierData, emtdata, epimutacionsData, FieldEffectCrc, GenomicDistributionsData, GSE103322, GSE13015, GSE62944, HDCytoData, HMP16SData, HumanAffyData, imcdatasets, mcsurvdata, MetaGxBreast, MetaGxOvarian, MetaGxPancreas, MethylSeqData, muscData, NxtIRFdata, ObMiTi, quantiseqr, restfulSEData, RLHub, sesameData, SimBenchData, SingleCellMultiModal, SingleMoleculeFootprintingData, spatialDmelxsim, STexampleData, TabulaMurisData, TabulaMurisSenisData, TENxVisiumData, tissueTreg, VectraPolarisData, xcoredata License: Artistic-2.0 MD5sum: b9ab8001f392152a6e2f975b55e634cb NeedsCompilation: no Package: iSEEu Version: 1.10.1 Depends: iSEE, iSEEhex Imports: methods, S4Vectors, IRanges, shiny, SummarizedExperiment, SingleCellExperiment, ggplot2, DT, stats, colourpicker, shinyAce Suggests: scRNAseq, scater, scran, airway, edgeR, AnnotationDbi, org.Hs.eg.db, GO.db, KEGGREST, knitr, igraph, rmarkdown, BiocStyle, htmltools, Rtsne, uwot, testthat (>= 2.1.0), covr License: MIT + file LICENSE MD5sum: 1f20cf472035d3056d883463bb82e325 NeedsCompilation: no Package: iSeq Version: 1.50.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 55d0b7391fbff7a965eaff42e4c762c5 NeedsCompilation: yes Package: ISLET Version: 1.0.0 Depends: R(>= 4.1.0), Matrix, parallel, BiocParallel, SummarizedExperiment, BiocGenerics Imports: stats, methods Suggests: BiocStyle, knitr, rmarkdown, htmltools, RUnit License: GPL-2 MD5sum: c4d134f388541417611a33e41843ead9 NeedsCompilation: no Package: isobar Version: 1.44.0 Depends: R (>= 2.10.0), Biobase, stats, methods Imports: distr, plyr, biomaRt, ggplot2 Suggests: MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS License: LGPL-2 MD5sum: 4ca2c276ba2edfd43c57bd939739db00 NeedsCompilation: no Package: IsoCorrectoR Version: 1.16.0 Depends: R (>= 3.5) Imports: dplyr, magrittr, methods, quadprog, readr, readxl, stringr, tibble, tools, utils, pracma, WriteXLS Suggests: IsoCorrectoRGUI, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 2b085e251e417eaa32adf60808eb0d8e NeedsCompilation: no Package: IsoCorrectoRGUI Version: 1.14.0 Depends: R (>= 3.6) Imports: IsoCorrectoR, readxl, tcltk2, tcltk, utils Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 5083f847eeece4e4c1a1eb6d5114e273 NeedsCompilation: no Package: IsoformSwitchAnalyzeR Version: 1.20.0 Depends: R (>= 3.6), limma, DEXSeq, ggplot2 Imports: methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>= 2.50.0), IRanges, GenomicRanges, DRIMSeq, RColorBrewer, rtracklayer, VennDiagram, DBI, grDevices, graphics, stats, utils, GenomeInfoDb, grid, tximport (>= 1.7.1), tximeta (>= 1.7.12), edgeR, futile.logger, stringr, dplyr, magrittr, readr, tibble, XVector, BiocGenerics, RCurl, Biobase Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown License: GPL (>= 2) MD5sum: 2efe2bf8079453afa4e6e8a84ee737fd NeedsCompilation: yes Package: ISoLDE Version: 1.26.0 Depends: R (>= 3.3.0),graphics,grDevices,stats,utils License: GPL (>= 2.0) MD5sum: 97f2847503cc9dd23922fa63aa4affec NeedsCompilation: yes Package: isomiRs Version: 1.26.0 Depends: R (>= 4.0), SummarizedExperiment Imports: AnnotationDbi, assertive.sets, BiocGenerics, Biobase, broom, cluster, cowplot, DEGreport, DESeq2, IRanges, dplyr, GenomicRanges, gplots, ggplot2, gtools, gridExtra, grid, grDevices, graphics, GGally, limma, methods, RColorBrewer, readr, reshape, rlang, stats, stringr, S4Vectors, tidyr, tibble Suggests: knitr, rmarkdown, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 36e1c4d3cbfb4726daa48661e5bbedda NeedsCompilation: no Package: ITALICS Version: 2.58.0 Depends: R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser, pd.mapping50k.xba240 Imports: affxparser, DBI, GLAD, oligo, oligoClasses, stats Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp License: GPL-2 MD5sum: c4aa57d40fd156f65b7e4e3789fe1670 NeedsCompilation: no Package: iterativeBMA Version: 1.56.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 32ca318882c77a1d89db66bb2ca93f6b NeedsCompilation: no Package: iterativeBMAsurv Version: 1.56.0 Depends: BMA, leaps, survival, splines Imports: graphics, grDevices, stats, survival, utils License: GPL (>= 2) MD5sum: 642bb275dd445cc856909ad88b9cc9bb NeedsCompilation: no Package: iterClust Version: 1.20.0 Depends: R (>= 3.4.1) Imports: Biobase, cluster, stats, methods Suggests: tsne, bcellViper License: file LICENSE MD5sum: d930534e998ab24935b2061ec8e407b8 NeedsCompilation: no Package: IVAS Version: 2.18.0 Depends: R (> 3.0.0),GenomicFeatures, ggplot2, Biobase Imports: doParallel, lme4, BiocGenerics, GenomicRanges, IRanges, foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, ggfortify, grDevices, methods, Matrix, BiocParallel,utils, stats Suggests: BiocStyle License: GPL-2 MD5sum: b19151888f26e7f8961f68c6afb66aef NeedsCompilation: no Package: ivygapSE Version: 1.20.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: shiny, survival, survminer, hwriter, plotly, ggplot2, S4Vectors, graphics, stats, utils, UpSetR Suggests: knitr, png, limma, grid, DT, randomForest, digest, testthat, rmarkdown License: Artistic-2.0 MD5sum: efc34e82eebaaa523f9b062c273949e3 NeedsCompilation: no Package: IWTomics Version: 1.22.0 Depends: R (>= 3.5.0), GenomicRanges Imports: parallel,gtable,grid,graphics,methods,IRanges,KernSmooth,fda,S4Vectors,grDevices,stats,utils,tools Suggests: knitr License: GPL (>= 2) MD5sum: 3fdd79bd52764b1a4c9ed66363150c2d NeedsCompilation: no Package: karyoploteR Version: 1.24.0 Depends: R (>= 3.4), regioneR, GenomicRanges, methods Imports: regioneR, GenomicRanges, IRanges, Rsamtools, stats, graphics, memoise, rtracklayer, GenomeInfoDb, S4Vectors, biovizBase, digest, bezier, GenomicFeatures, bamsignals, AnnotationDbi, grDevices, VariantAnnotation Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db, pasillaBamSubset License: Artistic-2.0 MD5sum: 0569368f4d39b2370a8c2f618fc04681 NeedsCompilation: no Package: katdetectr Version: 1.0.0 Depends: R (>= 4.2) Imports: BiocParallel (>= 1.26.2), changepoint (>= 2.2.3), changepoint.np (>= 1.0.3), checkmate (>= 2.0.0), dplyr (>= 1.0.8), GenomicRanges (>= 1.44.0), GenomeInfoDb (>= 1.28.4), IRanges (>= 2.26.0), maftools (>= 2.10.5), methods (>= 4.1.3), rlang (>= 1.0.2), S4Vectors (>= 0.30.2), tibble (>= 3.1.6), VariantAnnotation (>= 1.38.0), Biobase (>= 2.54.0), Rdpack (>= 2.3.1), ggplot2 (>= 3.3.5), tidyr (>= 1.2.0), BSgenome (>= 1.62.0), ggtext (>= 0.1.1), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.3), BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.4), plyranges (>= 1.17.0) Suggests: scales (>= 1.2.0), knitr (>= 1.37), rmarkdown (>= 2.13), testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: f64e184697904a747bd4c2dde5987ac4 NeedsCompilation: no Package: KBoost Version: 1.6.0 Depends: R (>= 4.1), stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 | GPL-3 MD5sum: 0a9650f874663e169cb961542c27dfd2 NeedsCompilation: no Package: KCsmart Version: 2.56.0 Depends: siggenes, multtest, KernSmooth Imports: methods, BiocGenerics Enhances: Biobase, CGHbase License: GPL-3 MD5sum: da0ce6a92f03b3830b227763cbdebc31 NeedsCompilation: no Package: kebabs Version: 1.32.0 Depends: R (>= 3.3.0), Biostrings (>= 2.35.5), kernlab Imports: methods, stats, Rcpp (>= 0.11.2), Matrix (>= 1.5-0), XVector (>= 0.7.3), S4Vectors (>= 0.27.3), e1071, LiblineaR, graphics, grDevices, utils, apcluster LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors Suggests: SparseM, Biobase, BiocGenerics, knitr License: GPL (>= 2.1) MD5sum: cfb970625761896bd8971487895fd3ac NeedsCompilation: yes Package: KEGGgraph Version: 1.58.3 Depends: R (>= 3.5.0) Imports: methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz Suggests: RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) MD5sum: fb4f53cd677272ac5729ff2e051bb24c NeedsCompilation: no Package: KEGGlincs Version: 1.24.0 Depends: R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db (>= 3.3.0) Imports: AnnotationDbi,KEGGgraph,igraph,plyr,gtools,httr,RJSONIO,KEGGREST, methods,graphics,stats,utils, XML, grDevices Suggests: BiocManager (>= 1.20.3), knitr, graph License: GPL-3 MD5sum: 9ec567d1ddb633385b7d7309604a73b5 NeedsCompilation: no Package: keggorthology Version: 2.50.0 Depends: R (>= 2.5.0),stats,graph,hgu95av2.db Imports: AnnotationDbi,graph,DBI, graph, grDevices, methods, stats, tools, utils Suggests: RBGL,ALL License: Artistic-2.0 MD5sum: 1c115179d4ba4bf8fcf198f0d7c0cce7 NeedsCompilation: no Package: KEGGREST Version: 1.38.0 Depends: R (>= 3.5.0) Imports: methods, httr, png, Biostrings Suggests: RUnit, BiocGenerics, knitr, markdown License: Artistic-2.0 MD5sum: 310e736e684002207adf8ee1350f2526 NeedsCompilation: no Package: KinSwingR Version: 1.16.0 Depends: R (>= 3.5) Imports: data.table, BiocParallel, sqldf, stats, grid, grDevices Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 9e48afd16af58f4ec324e96b867996e7 NeedsCompilation: no Package: kissDE Version: 1.18.0 Imports: aods3, Biobase, DESeq2, DSS, ggplot2, gplots, graphics, grDevices, matrixStats, stats, utils, foreach, doParallel, parallel, shiny, shinycssloaders, ade4, factoextra, DT Suggests: BiocStyle, testthat License: GPL (>= 2) MD5sum: 4c70aa04daa2c8f4050831fc629d5d4c NeedsCompilation: no Package: KnowSeq Version: 1.12.0 Depends: R (>= 4.0), cqn (>= 1.28.1) Imports: stringr, methods, ggplot2 (>= 3.3.0), jsonlite, kernlab, rlist, rmarkdown, reshape2, e1071, randomForest, caret, XML, praznik, R.utils, httr, sva (>= 3.30.1), edgeR (>= 3.24.3), limma (>= 3.38.3), grDevices, graphics, stats, utils, Hmisc (>= 4.4.0), gridExtra Suggests: knitr License: GPL (>= 2) MD5sum: a2347eabff59ff1e8447d7e0939263a7 NeedsCompilation: no Package: LACE Version: 2.2.0 Depends: R (>= 4.1.0) Imports: curl, igraph, foreach, doParallel, sortable, dplyr, data.tree, graphics, grDevices, parallel, RColorBrewer, Rfast, stats, SummarizedExperiment, utils, purrr, stringi, stringr, Matrix, tidyr, jsonlite, readr, configr, DT, tools, fs, data.table, htmltools, htmlwidgets, bsplus, shinyvalidate, shiny, shinythemes, shinyFiles, shinyjs, shinyBS, shinydashboard, biomaRt, callr, logr Suggests: BiocGenerics, BiocStyle, testthat, knitr, rmarkdown License: file LICENSE MD5sum: 1b5587f268daf05f93cacac41fbeb8b1 NeedsCompilation: no Package: lapmix Version: 1.64.0 Depends: R (>= 2.6.0),stats Imports: Biobase, graphics, grDevices, methods, stats, tools, utils License: GPL (>= 2) MD5sum: fed4c097468e8ec0fbb5a3fc29364518 NeedsCompilation: no Package: LBE Version: 1.66.0 Depends: stats Imports: graphics, grDevices, methods, stats, utils Suggests: qvalue License: GPL-2 MD5sum: c1cbdc3a3dcdf9f7e36030bb664c3586 NeedsCompilation: no Package: ldblock Version: 1.28.0 Depends: R (>= 3.5), methods, rlang Imports: BiocGenerics (>= 0.25.1), httr, Matrix Suggests: RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats, VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75, Rsamtools, GenomicFiles (>= 1.13.6) License: Artistic-2.0 MD5sum: d9007dd36c9a31da7126f72e09da0b1e NeedsCompilation: no Package: LEA Version: 3.10.2 Depends: R (>= 3.3.0), methods, stats, utils, graphics Suggests: knitr License: GPL-3 MD5sum: 6d7e5b285c8ee983f8bbd47cea5c2491 NeedsCompilation: yes Package: LedPred Version: 1.32.0 Depends: R (>= 3.2.0), e1071 (>= 1.6) Imports: akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl, ROCR, testthat License: MIT | file LICENSE MD5sum: ef273f5e578acd4de2ece11d890718e7 NeedsCompilation: no Package: lefser Version: 1.8.0 Depends: SummarizedExperiment, R (>= 4.0.0) Imports: coin, MASS, ggplot2, stats, methods Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle, testthat, pkgdown, covr, withr License: Artistic-2.0 MD5sum: 1b8bd9edb5471f8868e8b227c19a8a3e NeedsCompilation: no Package: les Version: 1.48.0 Depends: R (>= 2.13.2), methods, graphics, fdrtool Imports: boot, gplots, RColorBrewer Suggests: Biobase, limma Enhances: parallel License: GPL-3 MD5sum: 90402854310292fa4a78300bdf61d20a NeedsCompilation: no Package: levi Version: 1.16.0 Imports: DT(>= 0.4), RColorBrewer(>= 1.1-2), colorspace(>= 1.3-2), dplyr(>= 0.7.4), ggplot2(>= 2.2.1), httr(>= 1.3.1), igraph(>= 1.2.1), reshape2(>= 1.4.3), shiny(>= 1.0.5), shinydashboard(>= 0.7.0), shinyjs(>= 1.0), xml2(>= 1.2.0), knitr, Rcpp (>= 0.12.18), grid, grDevices, stats, utils, testthat, methods, rmarkdown LinkingTo: Rcpp Suggests: rmarkdown License: GPL (>= 2) MD5sum: 5d04bde0ec7292683758db61369402db NeedsCompilation: yes Package: lfa Version: 1.28.2 Depends: R (>= 3.2) Imports: corpcor Suggests: knitr, ggplot2 License: GPL-3 MD5sum: 83b9da84c5b1c85673d6635aeab0b167 NeedsCompilation: yes Package: limma Version: 3.54.2 Depends: R (>= 3.6.0) Imports: grDevices, graphics, stats, utils, methods Suggests: affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn License: GPL (>= 2) MD5sum: b669f0f8b3155c7b0ff778398af2243e NeedsCompilation: yes Package: limmaGUI Version: 1.74.0 Imports: methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot, xtable, utils License: GPL (>= 2) MD5sum: 714b5b58d0e19751378cc6d599aa71a1 NeedsCompilation: no Package: LineagePulse Version: 1.18.0 Imports: BiocParallel, circlize, compiler, ComplexHeatmap, ggplot2, gplots, grDevices, grid, knitr, Matrix, methods, RColorBrewer, SingleCellExperiment, splines, stats, SummarizedExperiment, utils License: Artistic-2.0 MD5sum: e2083dfd56710c44ae5e602e5ca155d4 NeedsCompilation: no Package: lineagespot Version: 1.2.0 Imports: VariantAnnotation, MatrixGenerics, SummarizedExperiment, data.table, stringr, httr, utils Suggests: BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a9cfcdf3ffb4afe7e02df0649eacf367 NeedsCompilation: no Package: LinkHD Version: 1.12.0 Depends: R(>= 3.6.0), methods, ggplot2, stats Imports: scales, cluster, graphics, ggpubr, gridExtra, vegan, rio, MultiAssayExperiment, emmeans, reshape2, data.table Suggests: MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: d76e67fc5d9d72967bfa831e3417dca3 NeedsCompilation: no Package: Linnorm Version: 2.22.2 Depends: R(>= 4.1.0) Imports: Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan, mclust, apcluster, ggplot2, ellipse, limma, utils, statmod, MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo, stats, amap, Rtsne, gmodels LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer, moments, testthat License: MIT + file LICENSE MD5sum: 666483ec9e91c2ce79583496d4499718 NeedsCompilation: yes Package: LinTInd Version: 1.2.0 Depends: R (>= 4.0), ggplot2, parallel, stats, S4Vectors Imports: data.tree, reshape2, networkD3, stringdist, purrr, ape, cowplot, ggnewscale, stringr, dplyr, rlist, pheatmap, Biostrings, IRanges, BiocGenerics(>= 0.36.1), ggtree Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 975f273e819bc5adb8a76c3aa9f60b1c NeedsCompilation: no Package: lionessR Version: 1.12.0 Depends: R (>= 3.6.0) Imports: stats, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, igraph, reshape2, limma, License: MIT + file LICENSE MD5sum: f4d319b98b7645b6646d50c4a7cb4dd4 NeedsCompilation: no Package: lipidr Version: 2.12.0 Depends: R (>= 3.6.0), SummarizedExperiment Imports: methods, stats, utils, data.table, S4Vectors, rlang, dplyr, tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD, magrittr Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, iheatmapr, spelling, testthat License: MIT + file LICENSE MD5sum: 4098a17c293c4e67d0042820b4f76235 NeedsCompilation: no Package: LiquidAssociation Version: 1.52.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>= 3) MD5sum: d5482c9c1e1f6e15722f1ea614518cb6 NeedsCompilation: no Package: lisaClust Version: 1.6.3 Depends: R (>= 4.0) Imports: ggplot2, class, concaveman, grid, BiocParallel, spatstat.explore, spatstat.geom, BiocGenerics, S4Vectors, methods, spicyR, purrr, stats, data.table, dplyr, tidyr, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, pheatmap Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 7aa111af5d8c32b065bb484f65534b95 NeedsCompilation: no Package: lmdme Version: 1.40.0 Depends: R (>= 2.14.1), pls, stemHypoxia Imports: stats, methods, limma Enhances: parallel License: GPL (>= 2) MD5sum: 4800afe9abb10aa3f0d1a42d719b06b4 NeedsCompilation: no Package: LOBSTAHS Version: 1.24.0 Depends: R (>= 3.4), xcms, CAMERA, methods Imports: utils Suggests: PtH2O2lipids, knitr, rmarkdown License: GPL (>= 3) + file LICENSE MD5sum: 04fe4db1bafa2094d2365d712327d078 NeedsCompilation: no Package: loci2path Version: 1.18.0 Depends: R (>= 3.5.0) Imports: pheatmap, wordcloud, RColorBrewer, data.table, methods, grDevices, stats, graphics, GenomicRanges, BiocParallel, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 14bba5d24c5bcdd0bf8efdffbf5577eb NeedsCompilation: no Package: logicFS Version: 2.18.0 Depends: LogicReg, mcbiopi, survival Imports: graphics, methods, stats Suggests: genefilter, siggenes License: LGPL (>= 2) MD5sum: 7d8fba23d13fb0b34f40fd6b474bd1d5 NeedsCompilation: no Package: logitT Version: 1.56.0 Depends: affy Suggests: SpikeInSubset License: GPL (>= 2) MD5sum: 4c6ae36074150dde94b426d46d1bdb00 NeedsCompilation: yes Package: LOLA Version: 1.28.0 Depends: R (>= 3.5.0) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, reshape2, utils, stats, methods Suggests: parallel, testthat, knitr, BiocStyle, rmarkdown Enhances: simpleCache, qvalue, ggplot2 License: GPL-3 MD5sum: e087859471c8aa8ec992d1d1c11d6a1a NeedsCompilation: no Package: LoomExperiment Version: 1.16.0 Depends: R (>= 3.5.0), S4Vectors, SingleCellExperiment, SummarizedExperiment, methods, rhdf5, BiocIO Imports: DelayedArray, GenomicRanges, HDF5Array, Matrix, stats, stringr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown, reticulate License: Artistic-2.0 MD5sum: da09acea19bde3869b0156d47b8d63f5 NeedsCompilation: no Package: LowMACA Version: 1.28.0 Depends: R (>= 2.10) Imports: cBioPortalData, parallel, stringr, reshape2, data.table, RColorBrewer, methods, LowMACAAnnotation, BiocParallel, motifStack, Biostrings, httr, grid, gridBase, plyr Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 00d852771a79338dfdd5f41318672af1 NeedsCompilation: no Package: LPE Version: 1.72.0 Depends: R (>= 2.10) Imports: stats License: LGPL MD5sum: d9444a8cb6eb53f557c137770ce62d6b NeedsCompilation: no Package: LPEadj Version: 1.58.0 Depends: LPE Imports: LPE, stats License: LGPL MD5sum: 584ded64033e6f6027a17014bcc2c48c NeedsCompilation: no Package: lpNet Version: 2.30.0 Depends: lpSolve License: Artistic License 2.0 MD5sum: 4a2ede12ed4410b3e3e3f162b91f6b02 NeedsCompilation: no Package: lpsymphony Version: 1.26.3 Depends: R (>= 3.0.0) Suggests: BiocStyle, knitr, testthat Enhances: slam License: EPL MD5sum: 625446c976c475cc3d7e4f203f6ff0d0 NeedsCompilation: yes Package: LRBaseDbi Version: 2.8.0 Depends: R (>= 3.5.0) Imports: methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase Suggests: testthat, BiocStyle License: Artistic-2.0 MD5sum: 480f81a7f4837f195832f4c2ec6e716a NeedsCompilation: no Package: LRcell Version: 1.6.0 Depends: R (>= 4.1), ExperimentHub, AnnotationHub Imports: BiocParallel, dplyr, ggplot2, ggrepel, magrittr, stats, utils Suggests: LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2, testthat License: MIT + file LICENSE MD5sum: b698cae5f254406d6f498bbcd32e08fa NeedsCompilation: no Package: lumi Version: 2.50.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Imports: affy (>= 1.23.4), methylumi (>= 2.3.2), GenomicFeatures, GenomicRanges, annotate, lattice, mgcv (>= 1.4-0), nleqslv, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, stats4, methods Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer License: LGPL (>= 2) MD5sum: 75798958630e07dd0a3553e8e95156a9 NeedsCompilation: no Package: LymphoSeq Version: 1.26.0 Depends: R (>= 3.3), LymphoSeqDB Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq, RColorBrewer, circlize, grid, utils, stats, ggtree, msa, Biostrings, phangorn, stringdist, UpSetR Suggests: knitr, pheatmap, wordcloud, rmarkdown License: Artistic-2.0 MD5sum: 0023046aac324a818c3aa01ce1e7c032 NeedsCompilation: no Package: M3C Version: 1.20.0 Depends: R (>= 3.5.0) Imports: ggplot2, Matrix, doSNOW, cluster, parallel, foreach, doParallel, matrixcalc, Rtsne, corpcor, umap Suggests: knitr, rmarkdown License: AGPL-3 MD5sum: ea89b608a44d9edf0e26e583f9abb42d NeedsCompilation: no Package: M3Drop Version: 1.24.0 Depends: R (>= 3.4), numDeriv Imports: RColorBrewer, gplots, bbmle, statmod, grDevices, graphics, stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods Suggests: ROCR, knitr, M3DExampleData, scater, SingleCellExperiment, monocle, Seurat, Biobase License: GPL (>= 2) MD5sum: 6cc8e23c85dfa49d27da4b66e21aabfe NeedsCompilation: no Package: m6Aboost Version: 1.4.0 Depends: S4Vectors, adabag, GenomicRanges, R (>= 4.1) Imports: dplyr, rtracklayer, BSgenome, Biostrings, utils, methods, IRanges, ExperimentHub Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: 7ea5d5c6ff5998fb5276e41ae7df09b1 NeedsCompilation: no Package: maanova Version: 1.68.2 Depends: R (>= 2.10) Imports: Biobase, graphics, grDevices, methods, stats, utils Suggests: qvalue, snow Enhances: Rmpi License: GPL (>= 2) MD5sum: 1c6c588f351f987b5cb1fb20a3a8a086 NeedsCompilation: yes Package: Maaslin2 Version: 1.12.0 Depends: R (>= 3.6) Imports: robustbase, biglm, pcaPP, edgeR, metagenomeSeq, lpsymphony, pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap, logging, data.table, lmerTest, hash, optparse, grDevices, stats, utils, glmmTMB, MASS, cplm, pscl, lme4 Suggests: knitr, testthat (>= 2.1.0), rmarkdown License: MIT + file LICENSE MD5sum: 5382ad81bbed778dd4ed9d62d8187647 NeedsCompilation: no Package: Macarron Version: 1.2.0 Depends: R (>= 4.2.0), SummarizedExperiment Imports: BiocParallel, DelayedArray, WGCNA, ff, data.table, dynamicTreeCut, Maaslin2, plyr, stats, psych, xml2, RCurl, RJSONIO, logging, methods, utils Suggests: knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown, markdown License: MIT + file LICENSE MD5sum: 349a19f62c6681aaeade9cde514a50bc NeedsCompilation: no Package: macat Version: 1.72.0 Depends: Biobase, annotate Suggests: hgu95av2.db, stjudem License: Artistic-2.0 MD5sum: 1096a9c3d1bf2b0ad6e691c1dd8aaf37 NeedsCompilation: no Package: maCorrPlot Version: 1.68.0 Depends: lattice Imports: graphics, grDevices, lattice, stats License: GPL (>= 2) MD5sum: a63b315e6d01de109ddf01556211ae69 NeedsCompilation: no Package: MACSQuantifyR Version: 1.12.0 Imports: readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel, methods, stats, latticeExtra, lattice, rmarkdown, png, grid, gridExtra, prettydoc, rvest, xml2 Suggests: knitr, testthat, R.utils, spelling License: Artistic-2.0 MD5sum: c2c457fbf33b0ddab74b1507899fa3ac NeedsCompilation: no Package: MACSr Version: 1.6.0 Depends: R (>= 4.1.0) Imports: utils, reticulate, S4Vectors, methods, basilisk, ExperimentHub, AnnotationHub Suggests: testthat, knitr, rmarkdown, BiocStyle, MACSdata License: BSD_3_clause + file LICENSE MD5sum: b8631d20e9b2bb9773294433427d871a NeedsCompilation: no Package: made4 Version: 1.72.0 Depends: RColorBrewer,gplots,scatterplot3d, Biobase, SummarizedExperiment Imports: ade4 Suggests: affy, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 73dcfb9909aeec72eec4682335e52eed NeedsCompilation: no Package: MADSEQ Version: 1.24.0 Depends: R (>= 3.5.0), rjags (>= 4.6) Imports: VGAM, coda, BSgenome, BSgenome.Hsapiens.UCSC.hg19, S4Vectors, methods, preprocessCore, GenomicAlignments, Rsamtools, Biostrings, GenomicRanges, IRanges, VariantAnnotation, SummarizedExperiment, GenomeInfoDb, rtracklayer, graphics, stats, grDevices, utils, zlibbioc, vcfR Suggests: knitr License: GPL (>= 2) MD5sum: 5ab12d023da164c0754fe94bf4bad8db NeedsCompilation: no Package: maftools Version: 2.14.0 Depends: R (>= 3.3) Imports: data.table, grDevices, methods, RColorBrewer, Rhtslib, survival, DNAcopy LinkingTo: Rhtslib, zlibbioc Suggests: berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors, pheatmap, curl License: MIT + file LICENSE MD5sum: c96cd10b50d6f0ed8296c5f0f93a5052 NeedsCompilation: yes Package: MAGAR Version: 1.6.0 Depends: R (>= 4.1), HDF5Array, RnBeads, snpStats, crlmm Imports: doParallel, igraph, bigstatsr, rjson, plyr, data.table, UpSetR, reshape2, jsonlite, methods, ff, argparse, impute, RnBeads.hg19, utils, stats Suggests: gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager License: GPL-3 MD5sum: d3bf94d2015c392cb7860f4e82b1b72d NeedsCompilation: no Package: MAGeCKFlute Version: 2.2.0 Depends: R (>= 4.1) Imports: Biobase, gridExtra, ggplot2, ggrepel, grDevices, grid, reshape2, stats, utils, DOSE, clusterProfiler, pathview, enrichplot, msigdbr, depmap Suggests: biomaRt, BiocStyle, dendextend, graphics, knitr, pheatmap, png, scales, sva, BiocManager License: GPL (>= 3) MD5sum: 603f82fd64bae38b73a12bf5ea8286b0 NeedsCompilation: no Package: magrene Version: 1.0.0 Depends: R (>= 4.2.0) Imports: utils, stats, BiocParallel Suggests: BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo, testthat (>= 3.0.0) License: GPL-3 MD5sum: 5ff36ac0d223dfb2748c00675385e43a NeedsCompilation: no Package: MAI Version: 1.4.0 Depends: R (>= 3.5.0) Imports: caret, parallel, doParallel, foreach, e1071, future.apply, future, missForest, pcaMethods, tidyverse, stats, utils, methods, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: afff79c1e82563cfafefa83b365508a3 NeedsCompilation: no Package: maigesPack Version: 1.62.0 Depends: R (>= 2.10), convert, graph, limma, marray, methods Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML, rgl, som License: GPL (>= 2) MD5sum: 97aedbad25ae29db86a1c2f6cc9a07c5 NeedsCompilation: yes Package: MAIT Version: 1.32.0 Depends: R (>= 2.10), CAMERA, Rcpp, pls Imports: gplots,e1071,class,MASS,plsgenomics,agricolae,xcms,methods,caret Suggests: faahKO Enhances: rgl License: GPL-2 MD5sum: b9bcf055609035513aacdca252e98bb9 NeedsCompilation: no Package: makecdfenv Version: 1.74.0 Depends: R (>= 2.6.0), affyio Imports: Biobase, affy, methods, stats, utils, zlibbioc License: GPL (>= 2) MD5sum: ec90875d67856eb2042bec906851da9c NeedsCompilation: yes Package: MANOR Version: 1.70.0 Depends: R (>= 2.10) Imports: GLAD, graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, bookdown License: GPL-2 MD5sum: 86328e070a9541927ab5d8072eb79f6f NeedsCompilation: yes Package: MantelCorr Version: 1.68.0 Depends: R (>= 2.10) Imports: stats License: GPL (>= 2) MD5sum: 6967eb1ffa9dd7ab516ad3bdac2d0403 NeedsCompilation: no Package: mAPKL Version: 1.28.0 Depends: R (>= 3.6.0), Biobase Imports: multtest, clusterSim, apcluster, limma, e1071, AnnotationDbi, methods, parmigene,igraph,reactome.db Suggests: BiocStyle, knitr, mAPKLData, hgu133plus2.db, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 8572304372e73ea0910184b2342910d0 NeedsCompilation: no Package: maPredictDSC Version: 1.36.0 Depends: R (>= 2.15.0), MASS,affy,limma,gcrma,ROC,class,e1071,caret,hgu133plus2.db,ROCR,AnnotationDbi,LungCancerACvsSCCGEO Suggests: parallel License: GPL-2 MD5sum: bb396b8e675728dcee062276413210fc NeedsCompilation: no Package: mapscape Version: 1.22.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), base64enc (>= 0.1-3), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 846c1f7cc1df376b746250585144331c NeedsCompilation: no Package: marr Version: 1.8.0 Depends: R (>= 4.0) Imports: Rcpp, SummarizedExperiment, utils, methods, ggplot2, dplyr, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, covr License: GPL (>= 3) MD5sum: 82706a852d843ae2106d68b822aa844a NeedsCompilation: yes Package: marray Version: 1.76.0 Depends: R (>= 2.10.0), limma, methods Suggests: tkWidgets License: LGPL MD5sum: 409204c0f7a5df93537c63e9d7018d4d NeedsCompilation: no Package: martini Version: 1.18.1 Depends: R (>= 4.0) Imports: igraph (>= 1.0.1), Matrix, memoise (>= 2.0.0), methods (>= 3.3.2), Rcpp (>= 0.12.8), snpStats (>= 1.20.0), stats, utils, LinkingTo: Rcpp, RcppEigen (>= 0.3.3.5.0) Suggests: biomaRt (>= 2.34.1), circlize (>= 0.4.11), STRINGdb (>= 2.2.0), httr (>= 1.2.1), IRanges (>= 2.8.2), S4Vectors (>= 0.12.2), knitr, testthat, readr, rmarkdown License: GPL-3 MD5sum: 3f1d00115ff5804bdbbbbe47f0dbc872 NeedsCompilation: yes Package: maser Version: 1.16.0 Depends: R (>= 3.5.0), ggplot2, GenomicRanges Imports: dplyr, rtracklayer, reshape2, Gviz, DT, GenomeInfoDb, stats, utils, IRanges, methods, BiocGenerics, parallel, data.table Suggests: testthat, knitr, rmarkdown, BiocStyle, AnnotationHub License: MIT + file LICENSE MD5sum: 091ac65e236509a216e877ff347c6055 NeedsCompilation: no Package: maSigPro Version: 1.70.0 Depends: R (>= 2.3.1) Imports: Biobase, graphics, grDevices, venn, mclust, stats, MASS License: GPL (>= 2) MD5sum: 805963ced65e6a497b27e0b0fbfb2bf3 NeedsCompilation: no Package: maskBAD Version: 1.42.0 Depends: R (>= 2.10), gcrma (>= 2.27.1), affy Suggests: hgu95av2probe, hgu95av2cdf License: GPL (>= 2) MD5sum: a07de67df0ce205e7a276fc12709d0b6 NeedsCompilation: no Package: MassArray Version: 1.50.0 Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, stats, utils License: GPL (>= 2) MD5sum: ca918721022f140429588476a9262781 NeedsCompilation: no Package: massiR Version: 1.34.0 Depends: cluster, gplots, diptest, Biobase, R (>= 3.0.2) Suggests: biomaRt, RUnit, BiocGenerics License: GPL-3 MD5sum: c109b811e70aba521dd4e28825ea0575 NeedsCompilation: no Package: MassSpecWavelet Version: 1.64.1 Suggests: signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench License: LGPL (>= 2) MD5sum: 9d63ad876e78f55716e99c9844c35607 NeedsCompilation: yes Package: MAST Version: 1.24.1 Depends: SingleCellExperiment (>= 1.2.0), R(>= 3.5) Imports: Biobase, BiocGenerics, S4Vectors, data.table, ggplot2, plyr, stringr, abind, methods, parallel, reshape2, stats, stats4, graphics, utils, SummarizedExperiment(>= 1.5.3), progress Suggests: knitr, rmarkdown, testthat, lme4(>= 1.0), blme, roxygen2(> 6.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF, TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer, BiocStyle, scater, DelayedArray, Matrix, HDF5Array, zinbwave, dplyr License: GPL (>= 2) MD5sum: 10506e9bc335f3fd25802ca5aabce102 NeedsCompilation: no Package: matchBox Version: 1.40.0 Depends: R (>= 2.8.0) License: Artistic-2.0 MD5sum: 417da5756e7ae1ef6c7ec7d91bd6ce97 NeedsCompilation: no Package: MatrixGenerics Version: 1.10.0 Depends: matrixStats (>= 0.60.1) Imports: methods Suggests: sparseMatrixStats, DelayedMatrixStats, SummarizedExperiment, testthat (>= 2.1.0), Matrix License: Artistic-2.0 MD5sum: d699dd28635bdee023a78d352c651bf2 NeedsCompilation: no Package: MatrixQCvis Version: 1.6.1 Depends: SummarizedExperiment (>= 1.20.0), plotly (>= 4.9.3), shiny (>= 1.6.0) Imports: ComplexHeatmap (>= 2.7.9), dplyr (>= 1.0.5), ggplot2 (>= 3.3.3), grDevices (>= 4.1.0), Hmisc (>= 4.5-0), htmlwidgets (>= 1.5.3), impute (>= 1.65.0), imputeLCMD (>= 2.0), limma (>= 3.47.12), MASS (>= 7.3-58.1), methods (>= 4.1.0), pcaMethods (>= 1.83.0), proDA (>= 1.5.0), rlang (>= 0.4.10), rmarkdown (>= 2.7), Rtsne (>= 0.15), shinydashboard (>= 0.7.1), shinyhelper (>= 0.3.2), shinyjs (>= 2.0.0), stats (>= 4.1.0), tibble (>= 3.1.1), tidyr (>= 1.1.3), umap (>= 0.2.7.0), UpSetR (>= 1.4.0), vsn (>= 3.59.1) Suggests: BiocGenerics (>= 0.37.4), BiocStyle (>= 2.19.2), hexbin (>= 1.28.2), knitr (>= 1.33), testthat (>= 3.0.2) License: GPL (>= 3) MD5sum: 04ee2f8908e11bd87ebe033bb5c6d1ff NeedsCompilation: no Package: MatrixRider Version: 1.30.0 Depends: R (>= 3.1.2) Imports: methods, TFBSTools, IRanges, XVector, Biostrings LinkingTo: IRanges, XVector, Biostrings, S4Vectors Suggests: RUnit, BiocGenerics, BiocStyle, JASPAR2014 License: GPL-3 MD5sum: 2f7739a0013d538ede275004afc6b7ff NeedsCompilation: yes Package: matter Version: 2.0.1 Depends: R (>= 3.5), BiocParallel, Matrix, methods, stats Imports: BiocGenerics, ProtGenerics, digest, irlba, biglm, utils Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: b72133dd10854e4847437c74723aa77f NeedsCompilation: yes Package: MBAmethyl Version: 1.32.0 Depends: R (>= 2.15) License: Artistic-2.0 MD5sum: 626fab9ef64ab97d9bb3a54a303b1c59 NeedsCompilation: no Package: MBASED Version: 1.32.0 Depends: RUnit, BiocGenerics, BiocParallel, GenomicRanges, SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: 62c450d62d07e35671f50afaff3e481b NeedsCompilation: no Package: MBCB Version: 1.52.0 Depends: R (>= 2.9.0), tcltk, tcltk2 Imports: preprocessCore, stats, utils License: GPL (>= 2) MD5sum: de89ddcb10aec57de534a5b9c077c1b3 NeedsCompilation: no Package: MBECS Version: 1.2.0 Depends: R (>= 4.1) Imports: methods, magrittr, phyloseq, limma, lme4, lmerTest, pheatmap, rmarkdown, cluster, dplyr, ggplot2, gridExtra, ruv, sva, tibble, tidyr, vegan, stats, utils, Matrix Suggests: knitr, markdown, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: b82851d33548f8a63ece200e01a81b9c NeedsCompilation: no Package: mbkmeans Version: 1.14.0 Depends: R (>= 3.6) Imports: methods, DelayedArray, Rcpp, S4Vectors, SingleCellExperiment, SummarizedExperiment, ClusterR, benchmarkme, Matrix, BiocParallel LinkingTo: Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR Suggests: beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown License: MIT + file LICENSE MD5sum: f349be5a250f06fc5b8a5b1aabd354b8 NeedsCompilation: yes Package: mbOmic Version: 1.2.0 Depends: R (>= 4.1.0) Imports: parallel, doParallel, psych, WGCNA, data.table, igraph, visNetwork, cluster, clusterSim, methods, graphics, stats Suggests: testthat (>= 3.0.0), knitr, rmarkdown, devtools, impute License: Artistic-2.0 MD5sum: 4e4e2dff7c987f29b65a42415193621e NeedsCompilation: no Package: mBPCR Version: 1.52.0 Depends: oligoClasses, GWASTools Imports: Biobase, graphics, methods, utils, grDevices Suggests: xtable License: GPL (>= 2) MD5sum: 1257ad22641e0de0f2f3d7b54b7b30fa NeedsCompilation: no Package: MBQN Version: 2.10.0 Depends: R (>= 3.6) Imports: stats, graphics, utils, limma (>= 3.30.13), SummarizedExperiment (>= 1.10.0), preprocessCore (>= 1.36.0), BiocFileCache, rappdirs, xml2, RCurl, ggplot2, PairedData, rmarkdown Suggests: knitr License: GPL-3 + file LICENSE MD5sum: 35da55cc00f00359c3c6620bcde393d3 NeedsCompilation: no Package: MBttest Version: 1.26.0 Depends: R (>= 3.3.0), stats, gplots, gtools,graphics,base, utils,grDevices Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: 7088560785d6a6276f86cead49f90ef5 NeedsCompilation: no Package: MCbiclust Version: 1.22.0 Depends: R (>= 3.4) Imports: BiocParallel, graphics, utils, stats, AnnotationDbi, GO.db, org.Hs.eg.db, GGally, ggplot2, scales, cluster, WGCNA Suggests: gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr, pander, devtools, testthat, GSVA License: GPL-2 MD5sum: 835a9f2ed663c29089258cb00e056f6a NeedsCompilation: no Package: mCSEA Version: 1.18.0 Depends: R (>= 3.5), mCSEAdata, Homo.sapiens Imports: biomaRt, fgsea, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, Gviz, IRanges, limma, methods, parallel, S4Vectors, stats, SummarizedExperiment, utils Suggests: Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k, knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit License: GPL-2 MD5sum: 37b5bf1c53d9fd57ca5d0aefd6da0262 NeedsCompilation: no Package: mdp Version: 1.18.0 Depends: R (>= 4.0) Imports: ggplot2, gridExtra, grid, stats, utils Suggests: testthat, knitr, rmarkdown, fgsea, BiocManager License: GPL-3 MD5sum: 7387ef3ab0e62a1006d02e00e3d9d3b6 NeedsCompilation: no Package: mdqc Version: 1.60.0 Depends: R (>= 2.2.1), cluster, MASS License: LGPL (>= 2) MD5sum: 8d82c7aba584e2523fc09bda2ba4f409 NeedsCompilation: no Package: MDTS Version: 1.18.0 Depends: R (>= 3.5.0) Imports: GenomicAlignments, GenomicRanges, IRanges, Biostrings, DNAcopy, Rsamtools, parallel, stringr Suggests: testthat, knitr License: Artistic-2.0 MD5sum: a552de65d5b110c862321a2bedaaea08 NeedsCompilation: no Package: MEAL Version: 1.28.0 Depends: R (>= 3.6.0), Biobase, MultiDataSet Imports: GenomicRanges, limma, vegan, BiocGenerics, minfi, IRanges, S4Vectors, methods, parallel, ggplot2 (>= 2.0.0), permute, Gviz, missMethyl, isva, SummarizedExperiment, SmartSVA, graphics, stats, utils, matrixStats Suggests: testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData, BiocStyle, rmarkdown, brgedata License: Artistic-2.0 MD5sum: 8d17ccdc765b89dccdfc4e71ff7d88ee NeedsCompilation: no Package: MeasurementError.cor Version: 1.70.0 License: LGPL MD5sum: df7c8bf4546ea1fcf5abc1ef2900ebbe NeedsCompilation: no Package: MEAT Version: 1.10.0 Depends: R (>= 4.0) Imports: impute (>= 1.58), dynamicTreeCut (>= 1.63), glmnet (>= 2.0), grDevices, graphics, stats, utils, stringr, tibble, RPMM (>= 1.25), minfi (>= 1.30), dplyr, SummarizedExperiment, wateRmelon Suggests: knitr, markdown, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 697c230d4cff7cccca0acbc5712f2d52 NeedsCompilation: no Package: MEB Version: 1.12.0 Depends: R (>= 3.6.0) Imports: e1071, SummarizedExperiment Suggests: knitr,rmarkdown,BiocStyle License: GPL-2 MD5sum: 377f8bcf1d05dca277ca4faa644cef3f NeedsCompilation: no Package: MEDIPS Version: 1.50.0 Depends: R (>= 3.0), BSgenome, Rsamtools Imports: GenomicRanges, Biostrings, graphics, gtools, IRanges, methods, stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer, preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle License: GPL (>= 2) MD5sum: 74a83e23eaceb74b612abcc98a88af9f NeedsCompilation: no Package: MEDME Version: 1.58.0 Depends: R (>= 2.15), grDevices, graphics, methods, stats, utils Imports: Biostrings, MASS, drc Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 License: GPL (>= 2) MD5sum: cb31997e1c89fe04653b1554848ed04a NeedsCompilation: yes Package: megadepth Version: 1.8.0 Imports: xfun, utils, fs, GenomicRanges, readr, cmdfun, dplyr, magrittr Suggests: covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer, derfinder, GenomeInfoDb, tools, RefManageR, testthat License: Artistic-2.0 MD5sum: 7117f19e94ae0ade0fd844097f15f2a5 NeedsCompilation: no Package: MEIGOR Version: 1.31.0 Depends: Rsolnp, snowfall, CNORode, deSolve Suggests: CellNOptR, knitr License: GPL-3 MD5sum: 50a47ae91d44e99d84fc830223aed148 NeedsCompilation: no Package: Melissa Version: 1.14.0 Depends: R (>= 3.5.0), BPRMeth, GenomicRanges Imports: data.table, parallel, ROCR, matrixcalc, mclust, ggplot2, doParallel, foreach, MCMCpack, cowplot, magrittr, mvtnorm, truncnorm, assertthat, BiocStyle, stats, utils Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: a02b9d9345b8937018fb1be05403ec4b NeedsCompilation: no Package: memes Version: 1.6.0 Depends: R (>= 4.1) Imports: Biostrings, dplyr, cmdfun (>= 1.0.2), GenomicRanges, ggplot2, ggseqlogo, magrittr, matrixStats, methods, patchwork, processx, purrr, rlang, readr, stats, tools, tibble, tidyr, utils, usethis, universalmotif (>= 1.9.3), xml2 Suggests: cowplot, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0), knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1), rmarkdown, covr License: MIT + file LICENSE MD5sum: cd87df8450ab4b31ed3be36ac4bd7ce1 NeedsCompilation: no Package: Mergeomics Version: 1.26.0 Depends: R (>= 3.0.1) Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: d3abc85630fc4589d351dd3e51621fdb NeedsCompilation: no Package: MeSHDbi Version: 1.34.0 Depends: R (>= 3.0.1) Imports: methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase Suggests: testthat License: Artistic-2.0 MD5sum: f352f912e56306ac1d3eafa4c9034abf NeedsCompilation: no Package: meshes Version: 1.24.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, DOSE, enrichplot, GOSemSim, methods, utils, AnnotationHub, MeSHDbi, yulab.utils Suggests: knitr, rmarkdown, prettydoc License: Artistic-2.0 MD5sum: 9b5827ad8c0fb6536efd04eaa78c098d NeedsCompilation: no Package: meshr Version: 2.4.0 Depends: R (>= 4.1.0) Imports: markdown, rmarkdown, BiocStyle, knitr, methods, stats, utils, fdrtool, MeSHDbi, Category, S4Vectors, BiocGenerics, RSQLite License: Artistic-2.0 MD5sum: 75e145adeff5dfbef95848ca41431bf4 NeedsCompilation: no Package: MesKit Version: 1.8.0 Depends: R (>= 4.0.0) Imports: methods, data.table, Biostrings, dplyr, tidyr (>= 1.0.0), ape (>= 5.4.1), ggrepel, pracma, ggridges, AnnotationDbi, IRanges, circlize, cowplot, mclust, phangorn, ComplexHeatmap (>= 1.9.3), ggplot2, RColorBrewer, grDevices, stats, utils, S4Vectors Suggests: shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), org.Hs.eg.db, clusterProfiler, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: d43a3e4893ddf2236ca7cb581c403eb3 NeedsCompilation: no Package: messina Version: 1.34.0 Depends: R (>= 3.1.0), survival (>= 2.37-4), methods Imports: Rcpp (>= 0.11.1), plyr (>= 1.8), ggplot2 (>= 0.9.3.1), grid (>= 3.1.0), foreach (>= 1.4.1), graphics LinkingTo: Rcpp Suggests: knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>= 2.22.0), BiocStyle Enhances: doMC (>= 1.3.3) License: EPL (>= 1.0) MD5sum: e12125306b13ef61e4b98dd3d9c1851b NeedsCompilation: yes Package: Metab Version: 1.32.0 Depends: xcms, R (>= 3.0.1), svDialogs Imports: pander Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: d2590780fb9463863f1b3c0a6c37c2f7 NeedsCompilation: no Package: metabCombiner Version: 1.8.0 Depends: R (>= 4.0), dplyr (>= 1.0) Imports: methods, mgcv, caret, S4Vectors, stats, utils, rlang, graphics, matrixStats, tidyr Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: eaaebdcaf1ea4f58ee9edf60bd9b9e6b NeedsCompilation: yes Package: metabinR Version: 1.0.0 Depends: R (>= 4.2) Imports: methods, rJava Suggests: BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, rmarkdown, sabre, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: 2f246dbf15e1c86236ad5a07e686e383 NeedsCompilation: no Package: MetaboAnnotation Version: 1.2.0 Depends: R (>= 4.0.0) Imports: BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics, methods, S4Vectors, Spectra (>= 1.7.2), BiocParallel, SummarizedExperiment, QFeatures, graphics, CompoundDb Suggests: testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, AnnotationHub Enhances: RMariaDB, RSQLite License: Artistic-2.0 MD5sum: 765d584f864fd68d19f39e7aded811ab NeedsCompilation: no Package: MetaboCoreUtils Version: 1.6.0 Depends: R (>= 4.0) Imports: utils, MsCoreUtils Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 7f8894003e45813e3b3b636a8e6c690c NeedsCompilation: no Package: metabolomicsWorkbenchR Version: 1.8.0 Depends: R (>= 4.0) Imports: data.table, httr, jsonlite, methods, MultiAssayExperiment, struct, SummarizedExperiment, utils Suggests: BiocStyle, covr, knitr, HDF5Array, rmarkdown, structToolbox, testthat, pmp, grid, png License: GPL-3 MD5sum: 98779e05a6ecaf5e96427b9783d2709f NeedsCompilation: no Package: metabomxtr Version: 1.32.0 Depends: methods,Biobase Imports: optimx, Formula, plyr, multtest, BiocParallel, ggplot2 Suggests: xtable, reshape2 License: GPL-2 MD5sum: 5c21ea442b80f415e609147d24c54420 NeedsCompilation: no Package: MetaboSignal Version: 1.28.0 Depends: R(>= 3.3) Imports: KEGGgraph, hpar, igraph, RCurl, KEGGREST, EnsDb.Hsapiens.v75, stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi, MWASTools, mygene Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 7753098e88b0645ce181a04b75e746d1 NeedsCompilation: no Package: metaCCA Version: 1.26.0 Suggests: knitr License: MIT + file LICENSE MD5sum: 2dd11c0a868cce00b1017b8b9307960b NeedsCompilation: no Package: MetaCyto Version: 1.20.0 Depends: R (>= 3.4) Imports: flowCore (>= 1.4),tidyr (>= 0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices, graphics, stats, utils Suggests: knitr, dplyr, rmarkdown License: GPL (>= 2) MD5sum: fd528475a5ee7f8d84e6db523f61eeb3 NeedsCompilation: no Package: metagene Version: 2.30.0 Depends: R (>= 3.5.0), R6 (>= 2.0), GenomicRanges, BiocParallel Imports: rtracklayer, gplots, tools, GenomicAlignments, GenomeInfoDb, GenomicFeatures, IRanges, ggplot2, Rsamtools, matrixStats, purrr, data.table, magrittr, methods, utils, ensembldb, EnsDb.Hsapiens.v86, stringr Suggests: BiocGenerics, similaRpeak, RUnit, knitr, BiocStyle, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: 44d4a58f2bc9eeafdf638408df47ad99 NeedsCompilation: no Package: metagene2 Version: 1.14.0 Depends: R (>= 4.0), R6 (>= 2.0), GenomicRanges, BiocParallel Imports: rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges, ggplot2, Rsamtools, purrr, data.table, methods, dplyr, magrittr, reshape2 Suggests: BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: b72b6a0fdcaba7a341f0498423558284 NeedsCompilation: no Package: metagenomeSeq Version: 1.40.0 Depends: R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer Imports: parallel, matrixStats, foreach, Matrix, gplots, graphics, grDevices, stats, utils, Wrench Suggests: annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW License: Artistic-2.0 MD5sum: 781b0ca9bd689236e6130ec81ce66998 NeedsCompilation: no Package: metahdep Version: 1.56.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 MD5sum: 3254dcdb515fa65cee397b399a41e8a1 NeedsCompilation: yes Package: metaMS Version: 1.34.0 Depends: R (>= 4.0), methods, CAMERA, xcms (>= 1.35) Imports: Matrix, tools, robustbase, BiocGenerics, graphics, stats, utils Suggests: metaMSdata, RUnit License: GPL (>= 2) MD5sum: 8b3004d0b568589b810c5629a0c3f449 NeedsCompilation: no Package: MetaNeighbor Version: 1.18.0 Depends: R(>= 3.5) Imports: grDevices, graphics, methods, stats (>= 3.4), utils (>= 3.4), Matrix (>= 1.2), matrixStats (>= 0.54), beanplot (>= 1.2), gplots (>= 3.0.1), RColorBrewer (>= 1.1.2), SummarizedExperiment (>= 1.12), SingleCellExperiment, igraph, dplyr, tidyr, tibble, ggplot2 Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2), UpSetR License: MIT + file LICENSE MD5sum: 047097b746bdb379a6ca23938eeb41ac NeedsCompilation: no Package: MetaPhOR Version: 1.0.0 Depends: R (>= 4.2.0) Imports: utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats, clusterProfiler, RecordLinkage, RCy3 Suggests: BiocStyle, knitr, rmarkdown, kableExtra License: Artistic-2.0 MD5sum: 62c0c64907ffe17e7ff61dfe5eb49a24 NeedsCompilation: no Package: metapod Version: 1.6.0 Imports: Rcpp LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 544ab23b2d3a4c6ec951080c4f485ef4 NeedsCompilation: yes Package: metapone Version: 1.4.0 Depends: R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea, ggplot2, ggrepel Imports: methods Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: cb7f29f1c0343c6b332a9f3b7fbec80a NeedsCompilation: no Package: metaSeq Version: 1.38.0 Depends: R (>= 2.13.0), NOISeq, snow, Rcpp License: Artistic-2.0 MD5sum: 926c2f82c7410bce7ebfa51e93895157 NeedsCompilation: no Package: metaseqR2 Version: 1.10.0 Depends: R (>= 4.0.0), DESeq2, limma, locfit, splines Imports: ABSSeq, baySeq, Biobase, BiocGenerics, BiocParallel, biomaRt, Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, gplots, graphics, grDevices, harmonicmeanp, heatmaply, htmltools, httr, IRanges, jsonlite, lattice, log4r, magrittr, MASS, Matrix, methods, NBPSeq, pander, parallel, qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite, rtracklayer, S4Vectors, stats, stringr, SummarizedExperiment, survcomp, utils, VennDiagram, vsn, yaml, zoo Suggests: BiocManager, BSgenome, knitr, RMySQL, RUnit Enhances: TCC License: GPL (>= 3) MD5sum: 12e54b517ff10bbb7f765ff325904823 NeedsCompilation: yes Package: metavizr Version: 1.21.0 Depends: R (>= 3.4), metagenomeSeq (>= 1.17.1), methods, data.table, Biobase, digest Imports: epivizr, epivizrData, epivizrServer, epivizrStandalone, vegan, GenomeInfoDb, phyloseq, httr Suggests: knitr, BiocStyle, matrixStats, msd16s (>= 0.109.1), etec16s, testthat, gss, ExperimentHub, tidyr, rmarkdown License: MIT + file LICENSE MD5sum: fd5ace5edab7af4671b13311b1b0aab4 NeedsCompilation: no Package: MetaVolcanoR Version: 1.12.0 Depends: R (>= 4.1.1) Imports: methods, data.table, dplyr, tidyr, plotly, ggplot2, cowplot, parallel, metafor, metap, rlang, topconfects, grDevices, graphics, stats, htmlwidgets Suggests: knitr, markdown, rmarkdown, testthat License: GPL-3 MD5sum: ac500cc922d3bc71ba24c1b76ab53285 NeedsCompilation: no Package: MetCirc Version: 1.28.0 Depends: R (>= 3.5), amap (>= 0.8), circlize (>= 0.3.9), scales (>= 0.3.0), shiny (>= 1.0.0), Spectra (>= 1.4.3) Imports: ggplot2 (>= 3.2.1), MsCoreUtils (>= 1.9.2), S4Vectors (>= 0.22.0) Suggests: BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr (>= 1.11), testthat (>= 2.2.1) License: GPL (>= 3) MD5sum: 66d09727991fe6ab93188f52f1a7f48e NeedsCompilation: no Package: MethCP Version: 1.11.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, S4Vectors, bsseq, DSS, methylKit, DNAcopy, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel Suggests: testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: bb85633025374d75480bc6ebc378e1a2 NeedsCompilation: no Package: methimpute Version: 1.20.0 Depends: R (>= 3.5.0), GenomicRanges, ggplot2 Imports: Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats, GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm, data.table LinkingTo: Rcpp Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: 2d5fa5fe9c7fe201f53af5561519b0ac NeedsCompilation: yes Package: methInheritSim Version: 1.20.0 Depends: R (>= 3.5.0) Imports: methylKit, GenomicRanges, GenomeInfoDb, parallel, BiocGenerics, S4Vectors, methods, stats, IRanges, msm Suggests: BiocStyle, knitr, rmarkdown, RUnit, methylInheritance License: Artistic-2.0 MD5sum: c1f975201f2fa7cfee6890e12fc0ef1b NeedsCompilation: no Package: MethPed Version: 1.26.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 MD5sum: af4c539faa889628f3a62a72292fc82d NeedsCompilation: no Package: MethReg Version: 1.8.0 Depends: R (>= 4.0) Imports: dplyr, plyr, GenomicRanges, SummarizedExperiment, DelayedArray, ggplot2, ggpubr, tibble, tidyr, S4Vectors, sesameData, sesame, AnnotationHub, ExperimentHub, stringr, readr, methods, stats, Matrix, MASS, rlang, pscl, IRanges, sfsmisc, progress, utils Suggests: rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, downloader, R.utils, doParallel, reshape2, JASPAR2022, TFBSTools, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr, jpeg, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: 93dfe428335da54d3cc959b5623140fb NeedsCompilation: no Package: methrix Version: 1.12.0 Depends: R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment Imports: rtracklayer, DelayedArray, HDF5Array, BSgenome, DelayedMatrixStats, parallel, methods, ggplot2, matrixStats, graphics, stats, utils, GenomicRanges, IRanges Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: fecc1dae6e67b793613f4e1eb62c2307 NeedsCompilation: no Package: MethTargetedNGS Version: 1.30.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings License: Artistic-2.0 MD5sum: e1a0275c0f8ae3004821d5d37635e171 NeedsCompilation: no Package: MethylAid Version: 1.32.0 Depends: R (>= 3.4) Imports: Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: 0328e8b4faf6fb81958299f2e622cf5a NeedsCompilation: no Package: methylCC Version: 1.12.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: CC BY 4.0 MD5sum: 370c98b0b66db5ef70157a92c16e2549 NeedsCompilation: no Package: methylclock Version: 1.4.0 Depends: R (>= 4.1.0), methylclockData, devtools, quadprog Imports: Rcpp (>= 1.0.6), ExperimentHub, dplyr, impute, PerformanceAnalytics, Biobase, ggpmisc, tidyverse, ggplot2, ggpubr, minfi, tibble, RPMM, stats, graphics, tidyr, gridExtra, preprocessCore, dynamicTreeCut, planet LinkingTo: Rcpp Suggests: BiocStyle, knitr, GEOquery, rmarkdown License: MIT + file LICENSE MD5sum: c33b21d106163a730dafd515dc4716cf NeedsCompilation: yes Package: methylGSA Version: 1.16.0 Depends: R (>= 3.5) Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, shiny, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr, rmarkdown, testthat, enrichplot License: GPL-2 MD5sum: bf2720c54865670d8495e478148d2d78 NeedsCompilation: no Package: methylInheritance Version: 1.22.0 Depends: R (>= 3.5) Imports: methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors, methods, parallel, ggplot2, gridExtra, rebus Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim License: Artistic-2.0 MD5sum: b39c2367bd3f224318ad8e9315ea7723 NeedsCompilation: no Package: methylKit Version: 1.24.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.18.1), methods Imports: IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>= 0.13.13), GenomeInfoDb, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager License: Artistic-2.0 MD5sum: b8bf98f842f90ab6e4759bf0711282e0 NeedsCompilation: yes Package: MethylMix Version: 2.28.0 Depends: R (>= 3.2.0) Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown License: GPL-2 MD5sum: 676e6ad64f624fe6bced99b03ca4b1d8 NeedsCompilation: no Package: methylMnM Version: 1.36.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: 9770923b1feb24d89c16cdab8bf12dbb NeedsCompilation: yes Package: methylPipe Version: 1.32.0 Depends: R (>= 3.5.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) MD5sum: 1eb838d98212f5df6771e7e0a9f10cb8 NeedsCompilation: yes Package: methylscaper Version: 1.6.0 Depends: R (>= 4.1.0) Imports: shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment Suggests: knitr, rmarkdown, devtools License: GPL-2 MD5sum: cc23579307bd57e74cd97b526a1618ea NeedsCompilation: no Package: MethylSeekR Version: 1.38.0 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), graphics (>= 2.15.2), grDevices (>= 2.15.2), parallel (>= 2.15.2), stats (>= 2.15.2), utils (>= 2.15.2) Suggests: BSgenome.Hsapiens.UCSC.hg18 License: GPL (>= 2) MD5sum: 2dcf909a7e64435d3c0f5a4c7f5fd70f NeedsCompilation: no Package: methylSig Version: 1.10.0 Depends: R (>= 3.6) Imports: bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, GenomeInfoDb, GenomicRanges, methods, parallel, stats, S4Vectors Suggests: BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr License: GPL-3 MD5sum: 92bc68749ca4fdfa145c3ef7c59323ee NeedsCompilation: no Package: methylumi Version: 2.44.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio, GenomicFeatures Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 MD5sum: 7f80c5b030cf4bb315423e21f3398913 NeedsCompilation: no Package: MetID Version: 1.16.0 Depends: R (>= 3.5) Imports: utils (>= 3.3.1), stats (>= 3.4.2), devtools (>= 1.13.0), stringr (>= 1.3.0), Matrix (>= 1.2-12), igraph (>= 1.2.1), ChemmineR (>= 2.30.2) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) License: Artistic-2.0 MD5sum: 58a99e831a5559c9c157f2f3db33421b NeedsCompilation: no Package: MetNet Version: 1.16.0 Depends: R (>= 4.0), S4Vectors (>= 0.28.1), SummarizedExperiment (>= 1.20.0) Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), corpcor (>= 1.6.10), dplyr (>= 1.0.3), ggplot2 (>= 3.3.3), GeneNet (>= 1.2.15), GENIE3 (>= 1.7.0), methods (>= 3.5), parmigene (>= 1.0.2), psych (>= 2.1.6), rlang (>= 0.4.10), stabs (>= 0.6), stats (>= 3.6), tibble (>= 3.0.5), tidyr (>= 1.1.2) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1), Spectra (>= 1.4.1), MsCoreUtils (>= 1.6.0) License: GPL (>= 3) MD5sum: f83206950d7f0fa7a2e3b62122035181 NeedsCompilation: no Package: mfa Version: 1.20.0 Depends: R (>= 3.4.0) Imports: methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack, MCMCglmm, coda, magrittr, tibble, Biobase LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: 05a223975c67fb8300c8ed545748a85c NeedsCompilation: yes Package: Mfuzz Version: 2.58.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 MD5sum: 49767b0d251d93740d749aec0b30f2eb NeedsCompilation: no Package: MGFM Version: 1.32.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 MD5sum: 336f0be43a2c223680559bf3c2f771dd NeedsCompilation: no Package: MGFR Version: 1.24.0 Depends: R (>= 3.5) Imports: biomaRt, annotate License: GPL-3 MD5sum: 602d734b6bd69c687c8d9d1600f95c9f NeedsCompilation: no Package: mgsa Version: 1.46.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: 8ced9f2d140d4c14f1fff69dfb679f49 NeedsCompilation: yes Package: mia Version: 1.6.0 Depends: R (>= 4.0), SummarizedExperiment, SingleCellExperiment, TreeSummarizedExperiment (>= 1.99.3), MultiAssayExperiment Imports: methods, stats, utils, MASS, ape, decontam, vegan, BiocGenerics, S4Vectors, IRanges, Biostrings, DECIPHER, BiocParallel, DelayedArray, DelayedMatrixStats, scuttle, scater, DirichletMultinomial, rlang, dplyr, tibble, tidyr Suggests: testthat, knitr, patchwork, BiocStyle, yaml, phyloseq, dada2, stringr, biomformat, reldist, ade4, microbiomeDataSets, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: addf1abe62527c86a77e7dce098c8f4d NeedsCompilation: no Package: miaSim Version: 1.4.0 Depends: SummarizedExperiment, TreeSummarizedExperiment Imports: deSolve, stats, poweRlaw, gtools, S4Vectors, MatrixGenerics Suggests: rmarkdown, knitr, BiocStyle, testthat License: Artistic-2.0 | file LICENSE MD5sum: 2799c0ad22de60cfa4463f37604eebcb NeedsCompilation: no Package: miaViz Version: 1.6.0 Depends: R (>= 4.0), SummarizedExperiment, TreeSummarizedExperiment, mia (>= 0.99), ggplot2, ggraph (>= 2.0) Imports: methods, stats, S4Vectors, BiocGenerics, BiocParallel, DelayedArray, scater, ggtree, ggnewscale, viridis, tibble, tidytree, tidygraph, rlang, purrr, tidyr, dplyr, ape, DirichletMultinomial Suggests: knitr, rmarkdown, BiocStyle, testthat, patchwork, microbiomeDataSets License: Artistic-2.0 | file LICENSE MD5sum: 8c72bf7cd69b58db6e4e9b2138f1e4e4 NeedsCompilation: no Package: MiChip Version: 1.52.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: b53a01c3859c397181c6ab483c19da4c NeedsCompilation: no Package: microbiome Version: 1.20.0 Depends: R (>= 3.6.0), phyloseq, ggplot2 Imports: Biostrings, compositions, dplyr, reshape2, Rtsne, scales, stats, tibble, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE MD5sum: c43968ac013d507e53ad62db6e172973 NeedsCompilation: no Package: microbiomeDASim Version: 1.12.0 Depends: R (>= 3.6.0) Imports: graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase Suggests: testthat (>= 2.1.0), knitr, devtools License: MIT + file LICENSE MD5sum: 35cff3663fc38b7de8dc1a3a3ae6a5fd NeedsCompilation: no Package: microbiomeExplorer Version: 1.8.0 Depends: shiny, magrittr, metagenomeSeq, Biobase Imports: shinyjs (>= 2.0.0), shinydashboard, shinycssloaders, shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer, dplyr, tidyr, purrr, rlang, knitr, readr, DT (>= 0.12.0), biomformat, tools, stringr, vegan, matrixStats, heatmaply, car, broom, limma, reshape2, tibble, forcats, lubridate, methods, plotly (>= 4.9.1) Suggests: V8, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 773c0a0ac1e0dc54b530fcf0c4258028 NeedsCompilation: no Package: microbiomeMarker Version: 1.4.0 Depends: R (>= 4.1.0) Imports: dplyr, phyloseq, magrittr, purrr, MASS, utils, ggplot2, tibble, rlang, stats, coin, ggtree, tidytree, methods, IRanges, tidyr, patchwork, ggsignif, metagenomeSeq, DESeq2, edgeR, BiocGenerics, Biostrings, yaml, biomformat, S4Vectors, Biobase, ComplexHeatmap, ANCOMBC, caret, limma, ALDEx2, multtest, plotROC, vegan, pROC, BiocParallel Suggests: testthat, covr, glmnet, Matrix, kernlab, e1071, ranger, knitr, rmarkdown, BiocStyle, withr License: GPL-3 MD5sum: 6e1ee6214cd3d90cc0224958866ad4b8 NeedsCompilation: no Package: MicrobiomeProfiler Version: 1.4.0 Depends: R (>= 4.1.0) Imports: clusterProfiler (>= 4.0.2), config, DT, enrichplot, golem, magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader, htmltools, ggplot2, graphics, utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-2 MD5sum: 3b2f44f617bb86f6733fe436a09de06a NeedsCompilation: no Package: MicrobiotaProcess Version: 1.10.3 Depends: R (>= 4.0.0) Imports: ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>= 1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, corrr, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial License: GPL (>= 3.0) MD5sum: 80e56ad826837b0f1768e0e30d30ee11 NeedsCompilation: no Package: microRNA Version: 1.56.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: 0db9d6be4a9f7499e050a5737a05848b NeedsCompilation: yes Package: midasHLA Version: 1.6.0 Depends: R (>= 4.1), MultiAssayExperiment (>= 1.8.3) Imports: assertthat (>= 0.2.0), broom (>= 0.5.1), dplyr (>= 0.8.0.1), formattable (>= 0.2.0.1), HardyWeinberg (>= 1.6.3), kableExtra (>= 1.1.0), knitr (>= 1.21), magrittr (>= 1.5), methods, stringi (>= 1.2.4), rlang (>= 0.3.1), S4Vectors (>= 0.20.1), stats, SummarizedExperiment (>= 1.12.0), tibble (>= 2.0.1), utils, qdapTools (>= 1.3.3) Suggests: broom.mixed (>= 0.2.4), cowplot (>= 1.0.0), devtools (>= 2.0.1), ggplot2 (>= 3.1.0), ggpubr (>= 0.2.5), rmarkdown, seqinr (>= 3.4-5), survival (>= 2.43-3), testthat (>= 2.0.1), tidyr (>= 1.1.2) License: MIT + file LICENCE MD5sum: a077050126dc237d2d1522ccfe471835 NeedsCompilation: no Package: MIGSA Version: 1.21.0 Depends: R (>= 3.4), methods, BiocGenerics Imports: AnnotationDbi, Biobase, BiocParallel, compiler, data.table, edgeR, futile.logger, ggdendro, ggplot2, GO.db, GOstats, graph, graphics, grDevices, grid, GSEABase, ismev, jsonlite, limma, matrixStats, org.Hs.eg.db, RBGL, reshape2, Rgraphviz, stats, utils, vegan Suggests: BiocStyle, breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, knitr, mGSZ, MIGSAdata, RUnit License: GPL (>= 2) MD5sum: f2db9241a0426842261c38f9399da681 NeedsCompilation: no Package: miloR Version: 1.6.0 Depends: R (>= 4.0.0), edgeR Imports: BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>= 1.3-0), S4Vectors, stats, stringr, methods, igraph, irlba, cowplot, BiocParallel, BiocSingular, limma, ggplot2, tibble, matrixStats, ggraph, gtools, SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices Suggests: testthat, MASS, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, curl, graphics License: GPL-3 + file LICENSE MD5sum: 4a6b1d138e8b16026e1d8328a92f81f1 NeedsCompilation: no Package: mimager Version: 1.22.0 Depends: Biobase Imports: BiocGenerics, S4Vectors, preprocessCore, grDevices, methods, grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 License: MIT + file LICENSE MD5sum: cecaf443f618e6d9b68cc808df98807f NeedsCompilation: no Package: MIMOSA Version: 1.36.0 Depends: R (>= 3.0.2), MASS, plyr, reshape, Biobase, ggplot2 Imports: methods, Formula, data.table, pracma, MCMCpack, coda, modeest, testthat, Rcpp, scales, dplyr, tidyr, rlang LinkingTo: Rcpp, RcppArmadillo Suggests: parallel, knitr License: MIT + file LICENSE MD5sum: b674eccd06b07947d8ba2620a3398c48 NeedsCompilation: yes Package: mina Version: 1.6.0 Depends: R (>= 4.0.0) Imports: methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory, foreach, ggplot2, parallel, parallelDist, reshape2, plyr, biganalytics, stringr, Hmisc, utils LinkingTo: Rcpp, RcppParallel, RcppArmadillo Suggests: knitr, rmarkdown Enhances: doMC License: GPL MD5sum: cbd92e6ffc537bc52b3a9137245cff0e NeedsCompilation: yes Package: MineICA Version: 1.38.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply Enhances: doMC License: GPL-2 MD5sum: 186df2862fd0a00c5177bcc091980aef NeedsCompilation: no Package: minet Version: 3.56.0 Imports: infotheo License: Artistic-2.0 MD5sum: 03df10c3ad62a7fd0f27d9ebc9965370 NeedsCompilation: yes Package: minfi Version: 1.44.0 Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges, SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>= 1.1.9) Imports: S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray (>= 0.15.16), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools License: Artistic-2.0 MD5sum: 890d1f3cbb088914bc0db16d0e178b27 NeedsCompilation: no Package: MinimumDistance Version: 1.42.0 Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1) Imports: methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: 65b928725f3e52f7530b8227e2d32266 NeedsCompilation: no Package: MiPP Version: 1.70.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: 0122b8eb3ab46046b573e6758a4b17d9 NeedsCompilation: no Package: miQC Version: 1.6.0 Depends: R (>= 3.5.0) Imports: SingleCellExperiment, flexmix, ggplot2, splines Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 02f1277f05c5eb3c8ec7b5d34e92fc9b NeedsCompilation: no Package: MIRA Version: 1.20.0 Depends: R (>= 3.5) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 1ffa63e33dedb1aed2e839e278a8a867 NeedsCompilation: no Package: MiRaGE Version: 1.40.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: BiocGenerics, S4Vectors, AnnotationDbi, BiocManager Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL MD5sum: 7c5dc2365d050d540270cbf2b96ada3d NeedsCompilation: no Package: miRBaseConverter Version: 1.22.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown License: GPL (>= 2) MD5sum: c022a54c4fbfe63559302943a5449416 NeedsCompilation: no Package: miRcomp Version: 1.28.0 Depends: R (>= 3.2), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: f96d242d0f8f015b23a865562733fe89 NeedsCompilation: no Package: mirIntegrator Version: 1.28.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: fe3209f40cf22714653bf412c94a62b7 NeedsCompilation: no Package: miRLAB Version: 1.28.0 Imports: methods, stats, utils, RCurl, httr, stringr, Hmisc, energy, entropy, gplots, glmnet, impute, limma, pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc, InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit,rmarkdown License: GPL (>= 2) MD5sum: 618d6e5f7e86ae9ad92a66f48fefb075 NeedsCompilation: no Package: miRmine Version: 1.20.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, DESeq2 License: GPL (>= 3) MD5sum: 799db6e6ba77d99fbbefb76fa25e2f38 NeedsCompilation: no Package: miRNAmeConverter Version: 1.26.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: d5d941c00a45e71aa7950bed9cc11275 NeedsCompilation: no Package: miRNApath Version: 1.58.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: aef82306383b07fc57ff69eb3aa57fa8 NeedsCompilation: no Package: miRNAtap Version: 1.32.0 Depends: R (>= 3.3.0), AnnotationDbi Imports: DBI, RSQLite, stringr, sqldf, plyr, methods Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat License: GPL-2 MD5sum: 0adca963228232d3eed8230401ebfad0 NeedsCompilation: no Package: miRSM Version: 1.16.0 Depends: R (>= 3.5.0) Imports: WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL, NMF, biclust, iBBiG, fabia, BicARE, isa2, s4vd, BiBitR, rqubic, Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero, ppclust, miRspongeR, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, MatrixCorrelation, energy Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: d889bed7ea716fb1c1d93e736b197fa4 NeedsCompilation: yes Package: miRspongeR Version: 2.2.0 Depends: R (>= 3.5.0) Imports: corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, linkcomm, utils, Rcpp, org.Hs.eg.db, foreach, doParallel Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 02afd81cc904ec994a3d34b7dee0247c NeedsCompilation: yes Package: mirTarRnaSeq Version: 1.6.0 Depends: R (>= 4.1.0), ggplot2 Imports: purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap, reshape2, corrplot, grDevices, graphics, stats, utils, data.table, R.utils Suggests: BiocStyle, knitr, rmarkdown, R.cache, SPONGE License: MIT + file LICENSE MD5sum: 816b561f506262e174f4077f7288893a NeedsCompilation: no Package: missMethyl Version: 1.32.1 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub License: GPL-2 MD5sum: 0e312da3c00ec9d012e93bd39b55f47c NeedsCompilation: no Package: missRows Version: 1.18.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 9e8586a06377cbc50361ec3d17546891 NeedsCompilation: no Package: mistyR Version: 1.6.1 Depends: R (>= 4.0) Imports: assertthat, caret, deldir, digest, distances, dplyr, filelock, furrr (>= 0.2.0), ggplot2, methods, purrr, ranger, readr (>= 2.0.0), ridge, rlang, rlist, R.utils, stats, stringr, tibble, tidyr, tidyselect (>= 1.2.0), utils, withr Suggests: BiocStyle, covr, earth, future, igraph (>= 1.2.7), iml, kernlab, knitr, MASS, rmarkdown, RSNNS, testthat (>= 3.0.0), xgboost License: GPL-3 MD5sum: dcbffd5985755f9fa83c80ef923808d9 NeedsCompilation: no Package: mitch Version: 1.10.0 Depends: R (>= 4.0) Imports: stats, grDevices, graphics, utils, MASS, plyr, reshape2, parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r Suggests: stringi, testthat (>= 2.1.0) License: CC BY-SA 4.0 + file LICENSE MD5sum: 61b7f17ae9e8a64a0dd745d9aa1c6608 NeedsCompilation: no Package: mitoClone2 Version: 1.4.0 Depends: R (>= 4.1.0) Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2 LinkingTo: Rhtslib (>= 1.13.1) Suggests: knitr, rmarkdown, Biostrings, testthat License: GPL-3 MD5sum: fdfd4eb3ec7d37bca9f071aaaf98be54 NeedsCompilation: yes Package: mixOmics Version: 6.22.0 Depends: R (>= 3.5.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, ggrepel, BiocParallel, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rgl License: GPL (>= 2) MD5sum: aa1c36cbe7e8e0a7a37083ab74944f79 NeedsCompilation: no Package: MLInterfaces Version: 1.78.0 Depends: R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4, tools, grDevices, graphics, stats, magrittr, SummarizedExperiment Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, testthat Enhances: parallel License: LGPL MD5sum: 536741263f88a52f9a393d5859e5442d NeedsCompilation: no Package: MLP Version: 1.46.0 Imports: AnnotationDbi, gplots, graphics, stats, utils Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, org.Mmu.eg.db, KEGGREST, annotate, Rgraphviz, GOstats, graph, limma, mouse4302.db, reactome.db License: GPL-3 MD5sum: 844ae3d974c32f6defd6a7dd29bff58f NeedsCompilation: no Package: MLSeq Version: 2.16.0 Depends: caret, ggplot2 Imports: testthat, VennDiagram, pamr, methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, e1071, kernlab License: GPL (>= 2) MD5sum: 8ebfbcfbb6fa1c9a7e853b284b106af6 NeedsCompilation: no Package: MMAPPR2 Version: 1.12.0 Depends: R (>= 3.6.0) Imports: ensemblVEP (>= 1.20.0), gmapR, Rsamtools, VariantAnnotation, BiocParallel, Biobase, BiocGenerics, dplyr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, tidyr, VariantTools, magrittr, methods, grDevices, graphics, stats, utils, stringr, data.table Suggests: testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle, MMAPPR2data License: GPL-3 OS_type: unix MD5sum: d35dd8072d88eebf402eff1483bcd724 NeedsCompilation: no Package: MMDiff2 Version: 1.26.0 Depends: R (>= 3.5.0), Rsamtools, Biobase Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 MD5sum: 36025b6b0186326f0c2cd3820d04b800 NeedsCompilation: no Package: MMUPHin Version: 1.12.1 Depends: R (>= 3.6) Imports: Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr, stringr, cowplot, utils, stats, grDevices Suggests: testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter License: MIT + file LICENSE MD5sum: e6dd325875529debae9076b245ee0a97 NeedsCompilation: no Package: mnem Version: 1.14.0 Depends: R (>= 4.1) Imports: cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071, ggplot2, wesanderson LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM License: GPL-3 MD5sum: d834503c0fd1ecfdb2b49da56b2d980d NeedsCompilation: yes Package: moanin Version: 1.6.0 Depends: R (>= 4.0), SummarizedExperiment, topGO, stats Imports: S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics, methods, grDevices, reshape2, NMI, zoo, ClusterR, splines, matrixStats Suggests: testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: 9c1b7197cfc9b9aa4f3441a6db647ba9 NeedsCompilation: no Package: MobilityTransformR Version: 1.2.0 Depends: MSnbase, R (>= 4.2) Imports: xcms, MetaboCoreUtils, Spectra Suggests: testthat, msdata (>= 0.35.3), knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown License: Artistic-2.0 MD5sum: 81d5f77198e6db54c7301db6a87354fe NeedsCompilation: no Package: MODA Version: 1.24.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 863743b3386a4fdece7e786d5f1f7fc9 NeedsCompilation: no Package: ModCon Version: 1.6.0 Depends: data.table, parallel, utils, stats, R (>= 4.1) Suggests: testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny, shinyFiles, shinydashboard, shinyjs License: GPL-3 + file LICENSE MD5sum: c90f43a74da5a77b665f2c4a2cca97fa NeedsCompilation: no Package: Modstrings Version: 1.14.0 Depends: R (>= 3.6), Biostrings (>= 2.51.5) Imports: methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 2659416d5be20fde27bcab5b7ee37aed NeedsCompilation: no Package: MOFA2 Version: 1.8.0 Depends: R (>= 4.0) Imports: rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods, RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array, grDevices, stats, magrittr, forcats, utils, corrplot, DelayedArray, Rtsne, uwot, basilisk, stringi Suggests: knitr, testthat, Seurat, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown License: file LICENSE MD5sum: 07111554b80efb5a6f13afab3908dcab NeedsCompilation: yes Package: MOGAMUN Version: 1.8.0 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: knitr, markdown License: GPL-3 + file LICENSE MD5sum: 2650c1d882e64ff1fed5a46afc552f87 NeedsCompilation: no Package: mogsa Version: 1.32.0 Depends: R (>= 3.4.0) Imports: methods, graphite, genefilter, BiocGenerics, gplots, GSEABase, Biobase, parallel, corpcor, svd, cluster, grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, org.Hs.eg.db License: GPL-2 MD5sum: f5a3ac58634e270b8b16a5a114f74d3d NeedsCompilation: no Package: MOMA Version: 1.10.0 Depends: R (>= 4.0) Imports: circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics, grid, grDevices, magrittr, methods, MKmisc, MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr, reshape2, rlang, stats, stringr, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, viper License: GPL-3 MD5sum: 12880abd652cc5fd253beb8846ebdc16 NeedsCompilation: no Package: monaLisa Version: 1.4.0 Depends: R (>= 4.1) Imports: methods, stats, utils, grDevices, graphics, BiocGenerics, GenomicRanges, TFBSTools, Biostrings, IRanges, stabs, BSgenome, glmnet, S4Vectors, SummarizedExperiment, BiocParallel, grid, circlize, ComplexHeatmap (>= 2.11.1), XVector, GenomeInfoDb, tools, vioplot Suggests: JASPAR2020, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat, BiocStyle, gridExtra License: GPL (>= 3) MD5sum: 9a731daa69f1272f7c2182d52398c7bf NeedsCompilation: no Package: monocle Version: 2.26.0 Depends: R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-6), DDRTree (>= 0.1.4), Imports: parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, Rtsne, MASS, reshape2, leidenbase (>= 0.1.9), limma, tibble, dplyr, qlcMatrix, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0) LinkingTo: Rcpp Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat License: Artistic-2.0 MD5sum: af246fb6ee2b887d62a568245dc47c7e NeedsCompilation: yes Package: MoonlightR Version: 1.24.0 Depends: R (>= 3.5), doParallel, foreach Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png License: GPL (>= 3) MD5sum: 57ce0d4904bbe180444e74d2e35e6b13 NeedsCompilation: no Package: mosaics Version: 2.36.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: 51393e2b668b86b00ae828177a9e8b35 NeedsCompilation: yes Package: mosbi Version: 1.4.0 Depends: R (>= 4.1) Imports: Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust, isa2, QUBIC, akmbiclust, RColorBrewer LinkingTo: Rcpp, BH, RcppParallel Suggests: knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 92da211f59f0b9f354ec33245ca38244 NeedsCompilation: yes Package: MOSim Version: 1.12.0 Depends: R (>= 3.6) Imports: HiddenMarkov, zoo, methods, matrixStats, dplyr, stringi, lazyeval, rlang, stats, utils, purrr, scales, stringr, tibble, tidyr, ggplot2, Biobase, IRanges, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 885623f05f8aaa564849e4988f49c49b NeedsCompilation: no Package: Motif2Site Version: 1.2.0 Depends: R (>= 4.1) Imports: S4Vectors, stats, utils, methods, grDevices, graphics, BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges, GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools Suggests: BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805 License: GPL-2 MD5sum: f0e170e90136ca550329605c691f71d9 NeedsCompilation: no Package: motifbreakR Version: 2.12.3 Depends: R (>= 4.1.0), grid, MotifDb Imports: methods, grDevices, stringr, parallel, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle License: GPL-2 MD5sum: f4bae4ef784e838affe4aef7db9ee743 NeedsCompilation: no Package: motifcounter Version: 1.22.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: 20feebf9276954794856bff8f95a52a6 NeedsCompilation: yes Package: MotifDb Version: 1.40.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes MD5sum: 3927588cd790546340de008fd2481d98 NeedsCompilation: no Package: motifmatchr Version: 1.20.0 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, GenomeInfoDb LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 + file LICENSE MD5sum: e934281fb8744d36f255bf4f3d71cd38 NeedsCompilation: yes Package: motifStack Version: 1.42.0 Depends: R (>= 2.15.1), methods, grid Imports: ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets, stats, stats4, utils, XML, TFBSTools Suggests: grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020 License: GPL (>= 2) MD5sum: 446df0cffd8663471bef7e94735b3b4b NeedsCompilation: no Package: MouseFM Version: 1.8.0 Depends: R (>= 4.0.0) Imports: httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales, gtools, tidyr, data.table, jsonlite, rlist, GenomeInfoDb, methods, biomaRt, stats, IRanges Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 2fc5307376b839f1ba11d13d9bb83806 NeedsCompilation: no Package: MPFE Version: 1.34.0 License: GPL (>= 3) MD5sum: e59a18a2268928f9957729c78ebf188a NeedsCompilation: no Package: mpra Version: 1.20.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, limma Imports: S4Vectors, scales, stats, graphics, statmod Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 9fde05e24c2ebcfb5f64451a50833191 NeedsCompilation: no Package: MPRAnalyze Version: 1.16.0 Imports: BiocParallel, methods, progress, stats, SummarizedExperiment Suggests: knitr License: GPL-3 MD5sum: 05a78c393a53d5adc5342c8045e6adec NeedsCompilation: no Package: MQmetrics Version: 1.6.0 Imports: ggplot2, readr, magrittr, dplyr, purrr, reshape2, gridExtra, utils, stringr, ggpubr, stats, cowplot, RColorBrewer, tidyr, scales, grid, rlang, ggforce, grDevices, gtable, plyr, knitr, rmarkdown, ggrepel, gghalves, tools Suggests: testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: 879b06ee1b711956dd33ce3acb8068ff NeedsCompilation: no Package: msa Version: 1.30.1 Depends: R (>= 3.3.0), methods, Biostrings (>= 2.40.0) Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors, tools LinkingTo: Rcpp Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn License: GPL (>= 2) MD5sum: 05f60762e9db486708261a5db83eefdb NeedsCompilation: yes Package: MSA2dist Version: 1.2.0 Depends: R (>= 4.2.0) Imports: Rcpp, Biostrings, GenomicRanges, IRanges, ape, doParallel, dplyr, foreach, methods, parallel, rlang, seqinr, stringr, tibble, tidyr, stats, stringi LinkingTo: Rcpp, RcppThread Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle License: GPL-3 + file LICENSE MD5sum: 9f8beef3590593304e45a90a6a22bdaa NeedsCompilation: yes Package: MsBackendMassbank Version: 1.6.1 Depends: R (>= 4.0), Spectra (>= 1.5.17) Imports: BiocParallel, S4Vectors, IRanges, methods, ProtGenerics, MsCoreUtils, DBI, utils Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, rmarkdown License: Artistic-2.0 MD5sum: 0b8bfe58c0843ef9aaeedae22863df1b NeedsCompilation: no Package: MsBackendMgf Version: 1.6.0 Depends: R (>= 4.0), Spectra (>= 1.5.14) Imports: BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown License: Artistic-2.0 MD5sum: bf1148385b65602b3480c9db6bf4e8e4 NeedsCompilation: no Package: MsBackendMsp Version: 1.2.0 Depends: R (>= 4.1.0), Spectra (>= 1.5.14) Imports: BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown License: Artistic-2.0 MD5sum: 96f533dfd6955624cb6ea70c6419dacb NeedsCompilation: no Package: MsBackendRawFileReader Version: 1.4.0 Depends: R (>= 4.1), methods, Spectra (>= 1.5.8) Imports: MsCoreUtils, S4Vectors, IRanges, rawrr (>= 1.3.6), utils, BiocParallel Suggests: BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr, lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat License: GPL-3 MD5sum: 368010c70d67f3febaecc347068f4c2b NeedsCompilation: yes Package: MsCoreUtils Version: 1.10.0 Depends: R (>= 3.6.0) Imports: methods, S4Vectors, MASS, stats, clue LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, pcaMethods, vsn, Matrix, preprocessCore, missForest Enhances: HDF5Array License: Artistic-2.0 MD5sum: de53cc4129c32af69cd6b1d7301a5e70 NeedsCompilation: yes Package: MsExperiment Version: 1.0.0 Depends: R (>= 4.2), ProtGenerics (>= 1.9.1), Imports: methods, S4Vectors, IRanges, Spectra, SummarizedExperiment, QFeatures Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown, rpx, mzR, msdata License: Artistic-2.0 MD5sum: 9ad2dfd41904028b925a6cd53bbddef8 NeedsCompilation: no Package: MsFeatures Version: 1.6.0 Depends: R (>= 4.1) Imports: methods, ProtGenerics (>= 1.23.5), MsCoreUtils, SummarizedExperiment, stats Suggests: testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown License: Artistic-2.0 MD5sum: c98bd9d75a340c91e7f5407268fc4665 NeedsCompilation: no Package: msgbsR Version: 1.22.0 Depends: R (>= 3.5.0), GenomicRanges, methods Imports: BSgenome, easyRNASeq, edgeR, GenomicAlignments, GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges, parallel, plyr, Rsamtools, R.utils, stats, SummarizedExperiment, S4Vectors, utils Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-2 MD5sum: 361adbeeca0b89ff5781311122349928 NeedsCompilation: no Package: msImpute Version: 1.8.0 Depends: R (>= 3.5.0) Imports: softImpute, methods, stats, graphics, pdist, reticulate, scran, data.table, FNN, matrixStats, limma, mvtnorm, tidyr, dplyr Suggests: BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD License: GPL (>= 2) MD5sum: 5a01888e2cec0c899c50e020be008920 NeedsCompilation: no Package: mslp Version: 1.0.2 Depends: R (>= 4.2.0), data.table (>= 1.13.0) Imports: doRNG, fmsb, foreach, magrittr, org.Hs.eg.db, pROC, randomForest, RankProd, stats, utils Suggests: BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2, tinytest License: GPL-3 MD5sum: e853879599d4200feed7f27eb5ec7ada NeedsCompilation: no Package: msmsEDA Version: 1.36.0 Depends: R (>= 3.0.1), MSnbase Imports: MASS, gplots, RColorBrewer License: GPL-2 MD5sum: 1db59be3d7ea20bdc4b3293d74cb44cb NeedsCompilation: no Package: msmsTests Version: 1.36.0 Depends: R (>= 3.0.1), MSnbase, msmsEDA Imports: edgeR, qvalue License: GPL-2 MD5sum: d6fcb6524c0eaee866ec79bc270b2c24 NeedsCompilation: no Package: MSnbase Version: 2.24.2 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.7.1), Biobase (>= 2.15.2), mzR (>= 2.29.3), S4Vectors, ProtGenerics (>= 1.29.1) Imports: MsCoreUtils, BiocParallel, IRanges (>= 2.13.28), plyr, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID (>= 1.5.2), digest, lattice, ggplot2, XML, scales, MASS, Rcpp LinkingTo: Rcpp Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr, SummarizedExperiment License: Artistic-2.0 MD5sum: be73d48936ab826ac6b03489c1ada7ba NeedsCompilation: yes Package: MSnID Version: 1.32.0 Depends: R (>= 2.10), Rcpp Imports: MSnbase (>= 1.12.1), mzID (>= 1.3.5), R.cache, foreach, doParallel, parallel, methods, iterators, data.table, Biobase, ProtGenerics, reshape2, dplyr, mzR, BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics, Biostrings, purrr, rlang, stringr, tibble, AnnotationHub, AnnotationDbi, xtable License: Artistic-2.0 MD5sum: a3fbc76e3678abed4b9837d7908a1523 NeedsCompilation: no Package: MSPrep Version: 1.8.0 Depends: R (>= 4.1.0) Imports: SummarizedExperiment, S4Vectors, pcaMethods (>= 1.24.0), crmn, preprocessCore, dplyr (>= 0.7), tidyr, tibble (>= 1.2), magrittr, rlang, stats, stringr, methods, missForest, sva, VIM, Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 1.0.2) License: GPL-3 MD5sum: ef7a1345f7a5e6cfaa0798d54072a579 NeedsCompilation: no Package: msPurity Version: 1.24.0 Depends: Rcpp Imports: plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite Suggests: MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL License: GPL-3 + file LICENSE MD5sum: 87acc64e53efae7328e2121a3e16a85d NeedsCompilation: no Package: msqrob2 Version: 1.6.1 Depends: R (>= 4.1), QFeatures (>= 1.1.2) Imports: stats, methods, lme4, purrr, BiocParallel, Matrix, MASS, limma, SummarizedExperiment, MultiAssayExperiment, codetools Suggests: multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata, MSnbase, matrixStats, MsCoreUtils, covr License: Artistic-2.0 MD5sum: cca88bb22aa157b11b5444245512523e NeedsCompilation: no Package: MSstats Version: 4.6.5 Depends: R (>= 4.0) Imports: MSstatsConvert, data.table, checkmate, MASS, limma, lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel, gplots, marray, stats, grDevices, graphics, methods, statmod LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, tinytest, covr, markdown License: Artistic-2.0 MD5sum: a7971a884a9581a7a1b0beb14cc40451 NeedsCompilation: yes Package: MSstatsConvert Version: 1.8.3 Depends: R (>= 4.0) Imports: data.table, log4r, methods, checkmate, utils, stringi Suggests: tinytest, covr, knitr, rmarkdown License: Artistic-2.0 MD5sum: 3d5774617ff3a9c7e9c222ee78e67d3d NeedsCompilation: no Package: MSstatsLiP Version: 1.4.1 Depends: R (>= 4.1) Imports: dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats, MSstatsConvert, data.table, Biostrings, MSstatsPTM, Rcpp, checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse, scales, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight License: Artistic-2.0 MD5sum: 241a15a910d7aef6a480056c58bdc651 NeedsCompilation: yes Package: MSstatsLOBD Version: 1.6.0 Depends: R (>= 4.0) Imports: minpack.lm, ggplot2, utils, stats, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr License: Artistic-2.0 MD5sum: fa80836576862fe29deeebca93a3d0e7 NeedsCompilation: no Package: MSstatsPTM Version: 2.0.3 Depends: R (>= 4.2) Imports: dplyr, gridExtra, stringr, stats, ggplot2, grDevices, MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp, Biostrings, checkmate, ggrepel LinkingTo: Rcpp Suggests: knitr, rmarkdown, tinytest, covr License: Artistic-2.0 MD5sum: 64d596c4355a1619d69463a86366d625 NeedsCompilation: yes Package: MSstatsQC Version: 2.16.0 Depends: R (>= 3.5.0) Imports: dplyr,plotly,ggplot2,ggExtra, stats,grid, MSnbase, qcmetrics Suggests: knitr,rmarkdown, testthat, RforProteomics License: Artistic License 2.0 MD5sum: 124330192d72e5ae986d5c4e2b80a6d0 NeedsCompilation: no Package: MSstatsQCgui Version: 1.18.0 Imports: shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid Suggests: knitr License: Artistic License 2.0 MD5sum: 0fde1a1850e1fe2bd0e6b2ccafb3e928 NeedsCompilation: no Package: MSstatsSampleSize Version: 1.12.0 Depends: R (>= 3.6) Imports: ggplot2, BiocParallel, caret, gridExtra, reshape2, stats, utils, grDevices, graphics, MSstats Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: dbfb1df46a9e01baab5a384e6ff952e8 NeedsCompilation: no Package: MSstatsShiny Version: 1.0.10 Depends: R (>= 4.2) Imports: shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2, data.table, Hmisc, MSstats, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, ggrepel, uuid, utils, stats, htmltools, methods, tidyr, grDevices, graphics Suggests: rmarkdown, tinytest, sessioninfo, knitr License: Artistic-2.0 MD5sum: 4e0564229ccace2b111e8e2be4ccbd57 NeedsCompilation: no Package: MSstatsTMT Version: 2.6.1 Depends: R (>= 4.2) Imports: limma, lme4, lmerTest, methods, data.table, stats, utils, ggplot2, grDevices, graphics, MSstats, MSstatsConvert, checkmate Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 3edaceb29f623d71576eca677e0e9da4 NeedsCompilation: no Package: MuData Version: 1.2.0 Depends: Matrix, S4Vectors, rhdf5 Imports: methods, stats, MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, DelayedArray Suggests: HDF5Array, rmarkdown, knitr, fs, testthat, BiocStyle, covr, SingleCellMultiModal, CiteFuse, scater License: GPL-3 MD5sum: 5d86826895ec779de269c50aaf347b29 NeedsCompilation: no Package: Mulcom Version: 1.48.0 Depends: R (>= 2.10), Biobase Imports: graphics, grDevices, stats, methods, fields License: GPL-2 MD5sum: 41674f0e93707fcbe2ec06e9c523b613 NeedsCompilation: yes Package: MultiAssayExperiment Version: 1.24.0 Depends: R (>= 4.2.0), SummarizedExperiment (>= 1.3.81) Imports: methods, GenomicRanges (>= 1.25.93), BiocBaseUtils, BiocGenerics, DelayedArray, S4Vectors (>= 0.23.19), IRanges, Biobase, stats, tidyr, utils Suggests: BiocStyle, HDF5Array (>= 1.19.17), knitr, maftools (>= 2.7.10), rmarkdown, R.rsp, RaggedExperiment, UpSetR, survival, survminer, testthat License: Artistic-2.0 MD5sum: 8fba9eac1903147a9cbf40dfe8ec9162 NeedsCompilation: no Package: MultiBaC Version: 1.8.0 Imports: Matrix, ggplot2, MultiAssayExperiment, ropls, graphics, methods, plotrix, grDevices, pcaMethods Suggests: knitr, rmarkdown, BiocStyle, devtools License: GPL-3 MD5sum: 10e45443f05de79a57e5f8869a4c0227 NeedsCompilation: no Package: multiClust Version: 1.28.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) MD5sum: 4cd925422c12ff049a1b487ea086c004 NeedsCompilation: no Package: multicrispr Version: 1.8.0 Depends: R (>= 4.0) Imports: assertive, BiocGenerics, Biostrings, BSgenome, CRISPRseek, data.table, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, grid, karyoploteR, magrittr, methods, parallel, plyranges, Rbowtie, reticulate, rtracklayer, stats, stringi, tidyr, tidyselect, utils Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, knitr, magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL-2 MD5sum: 02a2404864517558e021efec59eb93aa NeedsCompilation: no Package: MultiDataSet Version: 1.26.0 Depends: R (>= 4.1), Biobase Imports: BiocGenerics, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman, limma Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment License: file LICENSE MD5sum: 7df664216762ca1dc6e7e7a76516b9dd NeedsCompilation: no Package: multiGSEA Version: 1.8.2 Depends: R (>= 4.0.0) Imports: magrittr, graphite, AnnotationDbi, dplyr, fgsea, metap, rappdirs, rlang, methods Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, metaboliteIDmapping, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: GPL-3 MD5sum: afd0ff4c7eaea2209c9d53ea66ede688 NeedsCompilation: no Package: multiHiCcompare Version: 1.16.0 Depends: R (>= 4.0.0) Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 2559d4722bdf10329ab5b2e4f9303006 NeedsCompilation: no Package: MultiMed Version: 2.20.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE MD5sum: 955d70d0e50ad01d551ff391004d83d3 NeedsCompilation: no Package: multiMiR Version: 1.20.0 Depends: R (>= 3.4) Imports: stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 1.2), methods, BiocGenerics, AnnotationDbi, dplyr, Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) License: MIT + file LICENSE MD5sum: e828c9713bc9cd6be6545396da969f74 NeedsCompilation: no Package: multiOmicsViz Version: 1.22.0 Depends: R (>= 3.3.2) Imports: methods, parallel, doParallel, foreach, grDevices, graphics, utils, SummarizedExperiment, stats Suggests: BiocGenerics License: LGPL MD5sum: 2f7ff70ef162efe674e1caaba2fe4a23 NeedsCompilation: no Package: multiscan Version: 1.58.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) MD5sum: 0fbfbbc76d415635f71e58202f7d856f NeedsCompilation: yes Package: multiSight Version: 1.6.0 Depends: R (>= 4.1) Imports: golem, config, R6, shiny, shinydashboard, DT, dplyr, stringr, anyLib, caret, biosigner, mixOmics, stats, DESeq2, clusterProfiler, rWikiPathways, ReactomePA, enrichplot, ppcor, metap, infotheo, igraph, networkD3, easyPubMed, utils, htmltools, rmarkdown, ggnewscale Suggests: org.Mm.eg.db, rlang, markdown, attempt, processx, testthat, knitr, BiocStyle License: CeCILL + file LICENSE MD5sum: a98915438f0cd5efe7236ecad5630b18 NeedsCompilation: no Package: multtest Version: 2.54.0 Depends: R (>= 2.10), methods, BiocGenerics, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL MD5sum: dc67747ec97ee5a093d9cbf63db165fc NeedsCompilation: yes Package: mumosa Version: 1.6.0 Depends: SingleCellExperiment Imports: stats, utils, methods, igraph, Matrix, BiocGenerics, BiocParallel, IRanges, S4Vectors, DelayedArray, DelayedMatrixStats, SummarizedExperiment, BiocNeighbors, BiocSingular, ScaledMatrix, beachmat, scuttle, metapod, scran, batchelor, uwot Suggests: testthat, knitr, BiocStyle, rmarkdown, scater, bluster, DropletUtils, scRNAseq License: GPL-3 MD5sum: e73ff26cf2e2508548bf4e25734c3575 NeedsCompilation: no Package: MungeSumstats Version: 1.6.0 Depends: R(>= 4.1) Imports: magrittr, data.table, utils, R.utils, dplyr, stats, GenomicRanges, IRanges, GenomeInfoDb, BSgenome, Biostrings, stringr, VariantAnnotation, googleAuthR, httr, jsonlite, methods, parallel, rtracklayer, RCurl Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, Rsamtools, MatrixGenerics, badger, BiocParallel, GenomicFiles License: Artistic-2.0 MD5sum: 325f5862e6a05c1eddd929fa2031d83c NeedsCompilation: no Package: muscat Version: 1.12.1 Depends: R (>= 4.2) Imports: BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, S4Vectors, scales, scater, scuttle, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition, viridis Suggests: BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, testthat, UpSetR License: GPL-3 MD5sum: 2231991e13fd6fe7fa64e20084b486b4 NeedsCompilation: no Package: muscle Version: 3.40.0 Depends: Biostrings License: Unlimited MD5sum: 063dc9427f7c9770a8b1cae7903edf1b NeedsCompilation: yes Package: musicatk Version: 1.8.0 Depends: R (>= 4.0.0), NMF Imports: SummarizedExperiment, VariantAnnotation, cowplot, Biostrings, base, methods, magrittr, tibble, tidyr, gtools, gridExtra, MCMCprecision, MASS, matrixTests, data.table, dplyr, rlang, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, S4Vectors, uwot, ggplot2, stringr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, deconstructSigs, decompTumor2Sig, topicmodels, ggrepel, withr, plotly, utils, factoextra, cluster, ComplexHeatmap, philentropy, shinydashboard, sortable, maftools, shiny, shinyjs, shinyalert, shinybusy, shinyBS, TCGAbiolinks, shinyjqui, stringi Suggests: testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr License: LGPL-3 MD5sum: 6e648f5b8f29a024ad5bd257ed471930 NeedsCompilation: no Package: MutationalPatterns Version: 3.8.1 Depends: R (>= 4.2.0), GenomicRanges (>= 1.24.0), NMF (>= 0.20.6) Imports: stats, S4Vectors, BiocGenerics (>= 0.18.0), BSgenome (>= 1.40.0), VariantAnnotation (>= 1.18.1), dplyr (>= 0.8.3), tibble(>= 2.1.3), purrr (>= 0.3.2), tidyr (>= 1.0.0), stringr (>= 1.4.0), magrittr (>= 1.5), ggplot2 (>= 2.1.0), pracma (>= 1.8.8), IRanges (>= 2.6.0), GenomeInfoDb (>= 1.12.0), Biostrings (>= 2.40.0), ggdendro (>= 0.1-20), cowplot (>= 0.9.2), ggalluvial (>= 0.12.2), RColorBrewer, methods Suggests: BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), ccfindR (>= 1.6.0), GenomicFeatures, AnnotationDbi, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: ff3a022f803fea68752cd1e3529f178b NeedsCompilation: no Package: MVCClass Version: 1.72.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: 8d2bdf02c38adac4521340159fb18f2c NeedsCompilation: no Package: MWASTools Version: 1.22.0 Depends: R (>= 3.5.0) Imports: glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra, igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST, ComplexHeatmap, stats, utils Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: CC BY-NC-ND 4.0 MD5sum: 16c129f83577919dfc4443a2b71e7deb NeedsCompilation: no Package: mygene Version: 1.34.0 Depends: R (>= 3.2.1), GenomicFeatures, Imports: httr (>= 0.3), jsonlite (>= 0.9.7), S4Vectors, Hmisc, sqldf, plyr Suggests: BiocStyle License: Artistic-2.0 MD5sum: d6b637ff838fa5d7e12912878e8d380e NeedsCompilation: no Package: myvariant Version: 1.28.0 Depends: R (>= 3.2.1), VariantAnnotation Imports: httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, GenomeInfoDb Suggests: BiocStyle License: Artistic-2.0 MD5sum: 14657acfd1876685469119cf20b73b3b NeedsCompilation: no Package: mzID Version: 1.36.0 Depends: methods Imports: XML, plyr, parallel, doParallel, foreach, iterators, ProtGenerics Suggests: knitr, testthat License: GPL (>= 2) MD5sum: c61127d1e1a9e98c1f89fa02d7ba0c3d NeedsCompilation: no Package: mzR Version: 2.32.0 Depends: R (>= 4.0.0), Rcpp (>= 0.10.1), methods, utils Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3), ncdf4 LinkingTo: Rcpp, Rhdf5lib (>= 1.1.4) Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown License: Artistic-2.0 MD5sum: 9ae88dede29e362edba9ab68858a38c2 NeedsCompilation: yes Package: NADfinder Version: 1.22.0 Depends: R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, S4Vectors, SummarizedExperiment Imports: graphics, methods, baseline, signal, GenomicAlignments, GenomeInfoDb, rtracklayer, limma, trackViewer, stats, utils, Rsamtools, metap, EmpiricalBrownsMethod,ATACseqQC, corrplot, csaw Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager, rmarkdown License: GPL (>= 2) MD5sum: 5e5188173dba2b30d63142df8335d3a8 NeedsCompilation: no Package: NanoMethViz Version: 2.4.2 Depends: R (>= 4.0.0), methods, ggplot2 Imports: cpp11 (>= 0.2.5), readr, S4Vectors, SummarizedExperiment, BiocSingular, bsseq, forcats, assertthat, AnnotationDbi, Rcpp, dplyr, data.table, e1071, fs, GenomicRanges, ggrastr, glue, graphics, limma (>= 3.44.0), patchwork, purrr, rlang, R.utils, RSQLite, Rsamtools, scales (>= 1.2.0), scico, stats, stringr, tibble, tidyr, utils, withr, zlibbioc LinkingTo: Rcpp Suggests: DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr License: Apache License (>= 2.0) MD5sum: e335b5023ac96e95b570ec577908b3bc NeedsCompilation: yes Package: NanoStringDiff Version: 1.28.0 Depends: Biobase Imports: matrixStats, methods, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle License: GPL MD5sum: 3c9b3f3c442350bddfdce7ea57a39636 NeedsCompilation: yes Package: NanoStringNCTools Version: 1.6.1 Depends: R (>= 3.6), Biobase, S4Vectors, ggplot2 Imports: BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes, grDevices, IRanges, methods, pheatmap, RColorBrewer, stats, utils Suggests: biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf License: MIT MD5sum: d988ce152a99d853768d79aec106698e NeedsCompilation: no Package: NanoStringQCPro Version: 1.30.0 Depends: R (>= 3.2), methods Imports: AnnotationDbi (>= 1.26.0), org.Hs.eg.db (>= 2.14.0), Biobase (>= 2.24.0), knitr (>= 1.12), NMF (>= 0.20.5), RColorBrewer (>= 1.0-5), png (>= 0.1-7) Suggests: roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: ed7ff1dca1386be4f3bcaddf079ba067 NeedsCompilation: no Package: nanotatoR Version: 1.14.0 Depends: R (>= 4.1), Imports: hash(>= 2.2.6), openxlsx(>= 4.0.17), rentrez(>= 1.1.0), stats, rlang, stringr, knitr, testthat, utils, AnnotationDbi, httr, GenomicRanges, tidyverse, VarfromPDB, org.Hs.eg.db, curl, dplyr, XML, XML2R Suggests: rmarkdown, yaml License: file LICENSE MD5sum: f4add801d9f5be7743e5b22427dd6179 NeedsCompilation: no Package: NanoTube Version: 1.4.0 Depends: R (>= 4.1), Biobase, ggplot2, limma Imports: fgsea, methods, reshape, stats, utils Suggests: grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly, rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx License: GPL-3 + file LICENSE MD5sum: 06a5830db2f083f0fc705764df674a42 NeedsCompilation: no Package: NBAMSeq Version: 1.14.0 Depends: R (>= 3.6), SummarizedExperiment, S4Vectors Imports: DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods, stats, Suggests: knitr, rmarkdown, testthat, ggplot2 License: GPL-2 MD5sum: 86f836dfe9b4e1d16e52e803a7006d34 NeedsCompilation: no Package: NBSplice Version: 1.15.0 Depends: R (>= 3.5), methods Imports: edgeR, stats, MASS, car, mppa, BiocParallel, ggplot2, reshape2 Suggests: knitr, RUnit, BiocGenerics, BiocStyle, rmarkdown, markdown License: GPL (>= 2) MD5sum: 9c7fc77071d1c21ffda86d62fcda008b NeedsCompilation: no Package: ncdfFlow Version: 2.44.0 Depends: R (>= 2.14.0), flowCore(>= 1.51.7), methods, BH Imports: Biobase,BiocGenerics,flowCore,zlibbioc LinkingTo: cpp11,BH, Rhdf5lib Suggests: testthat,parallel,flowStats,knitr MD5sum: 24caf0dba4802c27180be2f7a7eb133a NeedsCompilation: yes Package: ncGTW Version: 1.12.0 Depends: methods, BiocParallel, xcms Imports: Rcpp, grDevices, graphics, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-2 MD5sum: 818305e642a0b0d4cee7026e2aab41bc NeedsCompilation: yes Package: NCIgraph Version: 1.46.0 Depends: R (>= 2.10.0) Imports: graph, KEGGgraph, methods, RBGL, RCy3, R.methodsS3 Suggests: Rgraphviz Enhances: DEGraph License: GPL-3 MD5sum: 59760cbed2c32b6220be0f40607b9b6e NeedsCompilation: no Package: ncRNAtools Version: 1.8.0 Imports: httr, xml2, utils, methods, grDevices, ggplot2, IRanges, GenomicRanges, S4Vectors Suggests: knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics License: GPL-3 MD5sum: a64aafbb2f826626d199d77de5465dfb NeedsCompilation: no Package: ndexr Version: 1.20.1 Depends: RCX Imports: httr, jsonlite, plyr, tidyr Suggests: BiocStyle, testthat, knitr, rmarkdown License: BSD_3_clause MD5sum: fc176737899996278d88c1ee56b72859 NeedsCompilation: no Package: nearBynding Version: 1.8.0 Depends: R (>= 4.0) Imports: R.utils, matrixStats, plyranges, transport, Rsamtools, S4Vectors, grDevices, graphics, rtracklayer, dplyr, GenomeInfoDb, methods, GenomicRanges, utils, stats, magrittr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, ggplot2, gplots, BiocGenerics, rlang Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 50a5c8c255d5023f3ae778db6027a995 NeedsCompilation: no Package: Nebulosa Version: 1.8.0 Depends: R (>= 4.0), ggplot2, patchwork Imports: Seurat, SingleCellExperiment, SummarizedExperiment, ks, Matrix, stats, methods Suggests: testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, SeuratObject License: GPL-3 MD5sum: 65d85f9bdeea5af2e5197f777d885483 NeedsCompilation: no Package: NeighborNet Version: 1.16.0 Depends: methods Imports: graph, stats License: CC BY-NC-ND 4.0 MD5sum: 8a264cc3bd45dd9414275aab20c9e085 NeedsCompilation: no Package: nempi Version: 1.6.0 Depends: R (>= 4.1), mnem Imports: e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats, epiNEM Suggests: knitr, BiocGenerics, rmarkdown, RUnit License: GPL-3 MD5sum: eb3e264895e520c00b2babd848eafcd6 NeedsCompilation: no Package: NetActivity Version: 1.0.0 Depends: R (>= 4.1.0) Imports: airway, DelayedArray, DelayedMatrixStats, DESeq2, methods, methods, NetActivityData, SummarizedExperiment, utils Suggests: AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse License: MIT + file LICENSE MD5sum: 40094b89a7632cb31f9566d3b828bbcc NeedsCompilation: no Package: netbiov Version: 1.31.0 Depends: R (>= 3.1.0), igraph (>= 0.7.1) Suggests: BiocStyle,RUnit,BiocGenerics,Matrix License: GPL (>= 2) MD5sum: d6911966ff8f74219e8087f6f0ea7a6a NeedsCompilation: no Package: netboost Version: 2.6.1 Depends: R (>= 4.0.0) Imports: Rcpp, RcppParallel, parallel, grDevices, graphics, stats, utils, dynamicTreeCut, WGCNA, impute, colorspace, methods, R.utils LinkingTo: Rcpp, RcppParallel Suggests: knitr, markdown, rmarkdown License: GPL-3 OS_type: unix MD5sum: 1d590bba5a6b1c2365dfa7eaf978a18d NeedsCompilation: yes Package: netboxr Version: 1.9.0 Depends: R (>= 4.0.0), igraph (>= 1.2.4.1), parallel Imports: RColorBrewer, DT, stats, clusterProfiler, data.table, gplots, jsonlite, plyr Suggests: paxtoolsr, BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, cgdsr License: LGPL-3 + file LICENSE MD5sum: 330e11b123222efb899fdbda87e62272 NeedsCompilation: no Package: netDx Version: 1.9.0 Depends: R (>= 3.6) Imports: ROCR,pracma,ggplot2,glmnet,igraph,reshape2, parallel,stats,utils,MultiAssayExperiment,graphics,grDevices, methods,BiocFileCache,GenomicRanges, bigmemory,doParallel,foreach, combinat,rappdirs,GenomeInfoDb,S4Vectors, IRanges,RColorBrewer,Rtsne,httr,plotrix Suggests: curatedTCGAData, rmarkdown, testthat, knitr, BiocStyle, RCy3, clusterExperiment, netSmooth, scater License: MIT + file LICENSE MD5sum: 8eca5eebaff3e1df575aa96dbb492abf NeedsCompilation: no Package: nethet Version: 1.30.0 Imports: glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network, ggplot2, grDevices, graphics, stats, utils Suggests: knitr, xtable, BiocStyle, testthat License: GPL-2 MD5sum: 8526c28e957cf9037965a950dedc41ba NeedsCompilation: yes Package: netOmics Version: 1.4.0 Depends: R (>= 4.1) Imports: dplyr, ggplot2, igraph, magrittr, minet, purrr, tibble, tidyr, AnnotationDbi, GO.db, RandomWalkRestartMH, gprofiler2, methods, stats Suggests: mixOmics, timeOmics, tidyverse, BiocStyle, testthat, covr, rmarkdown, knitr License: GPL-3 MD5sum: c4ad3bd9a8ac03b87bebc63a480ba919 NeedsCompilation: no Package: NetPathMiner Version: 1.34.2 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: d1ef3c92dd8901fc62744f2bc4c1bc92 NeedsCompilation: yes Package: netprioR Version: 1.24.0 Depends: methods, graphics, R(>= 3.3) Imports: stats, Matrix, dplyr, doParallel, foreach, parallel, sparseMVN, ggplot2, gridExtra, pROC Suggests: knitr, BiocStyle, pander License: GPL-3 MD5sum: 92f9247970d5719e68ed67e5d975e1e5 NeedsCompilation: no Package: netresponse Version: 1.58.0 Depends: R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods, minet, mclust, reshape2 Imports: ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer Suggests: knitr License: GPL (>= 2) MD5sum: b060124e28ae427e3870d8bafc382f76 NeedsCompilation: yes Package: NetSAM Version: 1.38.0 Depends: R (>= 3.0.0), seriation (>= 1.0-6), igraph (>= 0.6-1), tools (>= 3.0.0), WGCNA (>= 1.34.0), biomaRt (>= 2.18.0) Imports: methods, AnnotationDbi (>= 1.28.0), doParallel (>= 1.0.10), foreach (>= 1.4.0), survival (>= 2.37-7), GO.db (>= 2.10.0), R2HTML (>= 2.2.0), DBI (>= 0.5-1) Suggests: RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr, markdown License: LGPL MD5sum: cf65c21f15b5a0d7e1974a1444604a8c NeedsCompilation: no Package: netSmooth Version: 1.18.0 Depends: R (>= 3.5), scater (>= 1.15.11), clusterExperiment (>= 2.1.6) Imports: entropy, SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods, DelayedArray, HDF5Array (>= 1.15.13) Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot License: GPL-3 MD5sum: f71307c594d18c5289745ff32b7a39c9 NeedsCompilation: no Package: netZooR Version: 1.2.0 Depends: R (>= 4.2.0), igraph, reticulate, pandaR, yarn Imports: RCy3, viridisLite, STRINGdb, Biobase, GOstats, AnnotationDbi, matrixStats, GO.db, org.Hs.eg.db, Matrix, gplots, nnet, data.table, vegan, stats, utils, reshape, reshape2, penalized, parallel, doParallel, foreach, ggplot2, ggdendro, grid, MASS, assertthat, tidyr, methods, dplyr, graphics Suggests: testthat (>= 2.1.0), knitr, rmarkdown, pkgdown License: GPL-3 MD5sum: 321ba1f8cf38867733ad06da95546a4b NeedsCompilation: no Package: NeuCA Version: 1.4.0 Depends: R(>= 3.5.0), keras, limma, e1071, SingleCellExperiment Suggests: BiocStyle, knitr, rmarkdown, networkD3 License: GPL-2 MD5sum: 5313b43838e827fc634644c8c78c98f8 NeedsCompilation: no Package: NewWave Version: 1.8.0 Depends: R (>= 4.0), SummarizedExperiment Imports: methods, SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, SharedObject, stats Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr License: GPL-3 MD5sum: d130baf9dc1f65cf813c0ac810c08705 NeedsCompilation: no Package: ngsReports Version: 2.0.3 Depends: R (>= 4.2.0), BiocGenerics, ggplot2 (>= 3.4.0), patchwork (>= 1.1.1), tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 1.0.0), DT, forcats, ggdendro, grDevices (>= 3.6.0), grid, lifecycle, lubridate, methods, pander, plotly (>= 4.9.4), readr, reshape2, rlang, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo Suggests: BiocStyle, Cairo, knitr, testthat, truncnorm License: file LICENSE MD5sum: d4d7e4ca596e40ea607e88f0df4ff411 NeedsCompilation: no Package: nnNorm Version: 2.62.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: b760b319dd5b2636cd93ab2411602821 NeedsCompilation: no Package: nnSVG Version: 1.2.0 Depends: R (>= 4.2) Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods Suggests: BiocStyle, knitr, rmarkdown, STexampleData, scran, ggplot2, testthat License: MIT + file LICENSE MD5sum: d42af5f6f0c52ce3081fb37abf439706 NeedsCompilation: no Package: NOISeq Version: 2.42.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 MD5sum: 433f6d077210efad072673e9abda93fa NeedsCompilation: no Package: nondetects Version: 2.28.0 Depends: R (>= 3.2), Biobase (>= 2.22.0) Imports: limma, mvtnorm, utils, methods, arm, HTqPCR (>= 1.16.0) Suggests: knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics (>= 0.8.0) License: GPL-3 MD5sum: 21c17d748286c53340304be7077590d8 NeedsCompilation: no Package: NoRCE Version: 1.10.0 Depends: R (>= 4.2.0) Imports: KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,stringr,GenomeInfoDb, S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl, dbplyr,utils,ggplot2,igraph,stats,reshape2,readr, GO.db,zlibbioc, biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi Suggests: knitr, TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene, testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown, TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene, org.Mm.eg.db, org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics, org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, methods,markdown License: MIT + file LICENSE MD5sum: 0250f1d2e443bdb4393d29bba31ecaaa NeedsCompilation: no Package: normalize450K Version: 1.26.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 924352a1df046043ccd03fb808a40552 NeedsCompilation: no Package: NormalyzerDE Version: 1.16.0 Depends: R (>= 3.6) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, Biobase, RcmdrMisc, raster, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 MD5sum: 83bcaa765199205037e9c4d01167dc80 NeedsCompilation: no Package: NormqPCR Version: 1.44.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: d4d3aa3469db6111c010fff2ee691648 NeedsCompilation: no Package: normr Version: 1.24.0 Depends: R (>= 3.3.0) Imports: methods, stats, utils, grDevices, parallel, GenomeInfoDb, GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2), bamsignals (>= 1.4), rtracklayer (>= 1.32) LinkingTo: Rcpp Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown Enhances: BiocParallel License: GPL-2 MD5sum: ea7e051b690756e00a9ec7ec742f4f9b NeedsCompilation: yes Package: NPARC Version: 1.10.1 Depends: R (>= 4.0.0) Imports: dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr, stats, methods Suggests: testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2, BiocStyle License: GPL-3 MD5sum: 672dac7cf0b760c014bfab22bc1da289 NeedsCompilation: no Package: npGSEA Version: 1.34.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: d6b8f4012dbb085ae2ecf4519cdf2833 NeedsCompilation: no Package: NTW Version: 1.48.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 MD5sum: 91f8c0e9c074eacd20f850e9d9908c63 NeedsCompilation: no Package: nucleoSim Version: 1.26.0 Imports: stats, IRanges, S4Vectors, graphics, methods Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: edcd4a90610d012223c16bc66b9ee7ea NeedsCompilation: no Package: nucleR Version: 2.30.0 Depends: R (>= 3.5.0), methods Imports: Biobase, BiocGenerics, Biostrings, GenomeInfoDb, GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr, ggplot2, magrittr, parallel, stats, utils, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat License: LGPL (>= 3) MD5sum: 671e8b924067a623cc3f6b6444d51fd8 NeedsCompilation: no Package: nuCpos Version: 1.16.3 Depends: R (>= 4.2.0) Imports: graphics, methods Suggests: NuPoP, Biostrings, testthat License: GPL-2 MD5sum: 9deecfcda71cd4ebd342d4310d619f3b NeedsCompilation: yes Package: nullranges Version: 1.4.0 Imports: stats, IRanges, GenomicRanges, GenomeInfoDb, methods, rlang, S4Vectors, scales, InteractionSet, ggplot2, grDevices, plyranges, ks, speedglm, data.table, progress, ggridges Suggests: testthat, knitr, rmarkdown, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, nullrangesData, excluderanges, ensembldb, EnsDb.Hsapiens.v86, microbenchmark, patchwork, plotgardener, magrittr, tidyr, cobalt License: GPL-3 MD5sum: 3aa1affd80498c25281bc60321ecad08 NeedsCompilation: no Package: NuPoP Version: 2.6.3 Depends: R (>= 4.0) Imports: graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 2680307841955b92ccdca768ef16f715 NeedsCompilation: yes Package: NxtIRFcore Version: 1.4.0 Depends: R (>= 3.5.0), NxtIRFdata Imports: methods, stats, utils, tools, parallel, magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2, AnnotationHub, BiocFileCache, BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray, DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges, HDF5Array, IRanges, plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment, S4Vectors LinkingTo: Rcpp, zlibbioc, RcppProgress Suggests: knitr, rmarkdown, pheatmap, shiny, openssl, crayon, egg, DESeq2, limma, DoubleExpSeq, Rsubread, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: afc918ca864930fac309ccfb0a2a12e1 NeedsCompilation: yes Package: occugene Version: 1.58.0 Depends: R (>= 2.0.0) License: GPL (>= 2) MD5sum: be20bbf3dfe9ec4c2a1e1d292351a600 NeedsCompilation: no Package: OCplus Version: 1.72.0 Depends: R (>= 2.1.0) Imports: multtest (>= 1.7.3), graphics, grDevices, stats, interp License: LGPL MD5sum: 7ba11213670ceeb53f1cc9d15a217d30 NeedsCompilation: no Package: octad Version: 1.0.0 Depends: R (>= 4.2.0), magrittr, dplyr, ggplot2, edgeR, RUVSeq, DESeq2, limma, rhdf5, foreach, Rfast, octad.db, stats, httr, ExperimentHub, AnnotationHub, Biobase, S4Vectors Imports: EDASeq, GSVA, data.table, htmlwidgets, plotly, reshape2, grDevices, utils Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: b975f2e8d6df3f13b3e34dc2204052c3 NeedsCompilation: no Package: ODER Version: 1.4.0 Depends: R (>= 4.1) Imports: BiocGenerics, BiocFileCache, dasper, derfinder, dplyr, IRanges, GenomeInfoDb, GenomicRanges, ggplot2, ggpubr, ggrepel, magrittr, rtracklayer, S4Vectors, stringr, data.table, megadepth, methods, plyr, purrr, tibble, utils Suggests: BiocStyle, covr, knitr, recount, RefManageR, rmarkdown, sessioninfo, SummarizedExperiment, testthat (>= 3.0.0), GenomicFeatures, xfun License: Artistic-2.0 MD5sum: 849901628a61a7ea083ab06a26745dd4 NeedsCompilation: no Package: odseq Version: 1.26.0 Depends: R (>= 3.2.3) Imports: msa (>= 1.2.1), kebabs (>= 1.4.1), mclust (>= 5.1) Suggests: knitr(>= 1.11) License: MIT + file LICENSE MD5sum: 30cd1073e7924832ba39bdcf591fe6b3 NeedsCompilation: no Package: OGRE Version: 1.2.0 Depends: R (>= 4.1.0), S4Vectors Imports: GenomicRanges, methods, data.table, assertthat, ggplot2, Gviz, IRanges, AnnotationHub, grDevices, stats, GenomeInfoDb, shiny, shinyFiles, DT, rtracklayer, shinydashboard, shinyBS,tidyr Suggests: testthat (>= 3.0.0), knitr (>= 1.36), rmarkdown (>= 2.11) License: Artistic-2.0 MD5sum: 529ffcd31a1ed736f1144d6fce347e9b NeedsCompilation: no Package: oligo Version: 1.62.2 Depends: R (>= 3.2.0), BiocGenerics (>= 0.13.11), oligoClasses (>= 1.29.6), Biobase (>= 2.27.3), Biostrings (>= 2.35.12) Imports: affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, zlibbioc LinkingTo: preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl Enhances: doMC, doMPI License: LGPL (>= 2) MD5sum: 6b06135dd0df5f1d4116fa6fcf09ae59 NeedsCompilation: yes Package: oligoClasses Version: 1.60.0 Depends: R (>= 2.14) Imports: BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods, graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>= 1.23.2), foreach, BiocManager, utils, S4Vectors (>= 0.9.25), RSQLite, DBI, ff Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, VanillaICE, crlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) MD5sum: 950a81a0f6594b38b7cf294b761786ce NeedsCompilation: no Package: OLIN Version: 1.76.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 MD5sum: 36fce7f8e3e622d43d865acd7ffa3bf2 NeedsCompilation: no Package: OLINgui Version: 1.72.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 MD5sum: ecac686f9559ddce5a53d0310ee20dbc NeedsCompilation: no Package: omada Version: 1.0.0 Depends: pdfCluster (>= 1.0-3), kernlab (>= 0.9-29), R (>= 4.2), fpc (>= 2.2-9), Rcpp (>= 1.0.7), diceR (>= 0.6.0), ggplot2 (>= 3.3.5), reshape (>= 0.8.8), clusterCrit (>= 1.2.8), clValid (>= 0.7), glmnet (>= 4.1.3), dplyr(>= 1.0.7), stats (>= 4.1.2) Suggests: rmarkdown, knitr, testthat License: GPL-3 MD5sum: 3b2d84056e696e87e55dc340b8697f49 NeedsCompilation: no Package: OmaDB Version: 2.14.0 Depends: R (>= 3.5), httr (>= 1.2.1), plyr(>= 1.8.4) Imports: utils, ape, Biostrings, GenomicRanges, IRanges, methods, topGO, jsonlite Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: f857c3ef9976e930aae8ddca60207255 NeedsCompilation: no Package: omicade4 Version: 1.38.0 Depends: R (>= 3.0.0), ade4 Imports: made4, Biobase Suggests: BiocStyle License: GPL-2 MD5sum: c9dc47612e55ed92116cad4a755ed029 NeedsCompilation: no Package: OmicCircos Version: 1.36.0 Depends: R (>= 2.14.0), methods,GenomicRanges License: GPL-2 MD5sum: 581d681adc8453d5a5d5179d76087b9a NeedsCompilation: no Package: omicplotR Version: 1.18.0 Depends: R (>= 3.6), ALDEx2 (>= 1.18.0) Imports: compositions, DT, grDevices, knitr, jsonlite, matrixStats, rmarkdown, shiny, stats, vegan, zCompositions License: MIT + file LICENSE MD5sum: efffb7c37c2fcf5a62b56daf54d63a12 NeedsCompilation: no Package: omicRexposome Version: 1.20.0 Depends: R (>= 3.5.0), Biobase Imports: stats, utils, grDevices, graphics, methods, rexposome, limma, sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet, SmartSVA, isva, parallel, SummarizedExperiment, stringr Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata License: MIT + file LICENSE MD5sum: 9a65650e556e8dbb9819982270d9e986 NeedsCompilation: no Package: OmicsLonDA Version: 1.14.0 Depends: R(>= 3.6) Imports: SummarizedExperiment, gss, plyr, zoo, pracma, ggplot2, BiocParallel, parallel, grDevices, graphics, stats, utils, methods, BiocGenerics Suggests: knitr, rmarkdown, testthat, devtools, BiocManager License: MIT + file LICENSE MD5sum: 6498b69f43563fe73ea5c4fbde7f1872 NeedsCompilation: no Package: OMICsPCA Version: 1.16.0 Depends: R (>= 3.5.0), OMICsPCAdata Imports: HelloRanges, fpc, stats, MultiAssayExperiment, pdftools, methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown, kableExtra, rtracklayer, IRanges, GenomeInfoDb, reshape2, ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR, PerformanceAnalytics, tidyr, data.table, cluster, magick Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 2a9dbe435f1bb09185da740972988f06 NeedsCompilation: no Package: omicsPrint Version: 1.18.0 Depends: R (>= 3.5), MASS Imports: methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 2) MD5sum: 3dd8e7e97050a0593e821e1a9693066d NeedsCompilation: no Package: omicsViewer Version: 1.2.0 Depends: R (>= 4.2) Imports: survminer, survival, fastmatch, reshape2, stringr, beeswarm, grDevices, DT, shiny, shinythemes, shinyWidgets, plotly, networkD3, httr, matrixStats, RColorBrewer, Biobase, fgsea, openxlsx, psych, shinybusy, ggseqlogo, htmlwidgets, graphics, grid, stats, utils, methods, shinyjs, curl, flatxml, ggplot2, S4Vectors, SummarizedExperiment, RSQLite, Matrix, shinycssloaders Suggests: BiocStyle, knitr, rmarkdown, unittest License: GPL-2 MD5sum: b6d8a0ba853c8953e37181519b9dd6b5 NeedsCompilation: no Package: Omixer Version: 1.8.0 Depends: R (>= 4.0.0) Imports: dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr, tidyselect, grid, stats, stringr Suggests: knitr, rmarkdown, BiocStyle, magick, testthat License: MIT + file LICENSE MD5sum: 3e969b34b779b0f9ebc26f031e4d5163 NeedsCompilation: no Package: OmnipathR Version: 3.5.25 Depends: R(>= 4.0) Imports: checkmate, crayon, curl, digest, dplyr, httr, igraph, jsonlite, later, logger, magrittr, progress, purrr, rappdirs, readr(>= 2.0.0), readxl, rlang, rmarkdown, rvest, stats, stringr, tibble, tidyr, tidyselect, tools, utils, withr, xml2, yaml Suggests: BiocStyle, biomaRt, bookdown, dnet, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, smoof, supraHex, testthat License: MIT + file LICENSE MD5sum: 97f1a0eba3aaf914892cd974c6175f0c NeedsCompilation: no Package: ompBAM Version: 1.2.0 Imports: utils, Rcpp, zlibbioc Suggests: RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 885c1ca56ac6107961f421b118f7ff73 NeedsCompilation: no Package: oncomix Version: 1.20.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: 2dab4409041a3d92c2ee2aaf18b42096 NeedsCompilation: no Package: oncoscanR Version: 1.0.0 Depends: R (>= 4.2), IRanges (>= 2.30.0), GenomicRanges (>= 1.48.0), magrittr Imports: readr, S4Vectors, methods, utils Suggests: testthat (>= 3.1.4), jsonlite, knitr, rmarkdown License: MIT + file LICENSE MD5sum: ac3eafa3f9413fd81ecb2f1f0707b1d1 NeedsCompilation: no Package: OncoScore Version: 1.26.0 Depends: R (>= 4.1.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: 617467cd0166870b3acb68a0a9365feb NeedsCompilation: no Package: OncoSimulR Version: 4.0.2 Depends: R (>= 3.5.0) Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel, stringr LinkingTo: Rcpp Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander License: GPL (>= 3) MD5sum: 0b3c2e89633b0f157f176814aa90df1b NeedsCompilation: yes Package: oneSENSE Version: 1.20.0 Depends: R (>= 3.4), webshot, shiny, shinyFiles, scatterplot3d Imports: Rtsne, plotly, gplots, grDevices, graphics, stats, utils, methods, flowCore Suggests: knitr, rmarkdown License: GPL (>= 3) MD5sum: c89540d29c09f4cb0e00a650ca5a7f20 NeedsCompilation: no Package: onlineFDR Version: 2.6.0 Imports: stats, Rcpp, progress LinkingTo: Rcpp, RcppProgress Suggests: knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: d692b479ec2674b46a49b0386981ea0a NeedsCompilation: yes Package: ontoProc Version: 1.20.0 Depends: R (>= 4.0), ontologyIndex Imports: Biobase, S4Vectors, methods, stats, utils, BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph, AnnotationHub, SummarizedExperiment Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi License: Artistic-2.0 MD5sum: 1daa3e60bc2f12b3520325da46d0b57b NeedsCompilation: no Package: openCyto Version: 2.10.1 Depends: R (>= 3.5.0) Imports: methods,Biobase,BiocGenerics,flowCore(>= 1.99.17),flowViz,ncdfFlow(>= 2.11.34),flowWorkspace(>= 3.99.1),flowClust(>= 3.11.4),RBGL,graph,data.table,RColorBrewer LinkingTo: cpp11, BH Suggests: flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS MD5sum: be2c71e5a91bed8100704ea41696494a NeedsCompilation: yes Package: openPrimeR Version: 1.20.0 Depends: R (>= 4.0.0) Imports: Biostrings (>= 2.38.4), XML (>= 3.98-1.4), scales (>= 0.4.0), reshape2 (>= 1.4.1), seqinr (>= 3.3-3), IRanges (>= 2.4.8), GenomicRanges (>= 1.22.4), ggplot2 (>= 2.1.0), plyr (>= 1.8.4), dplyr (>= 0.5.0), stringdist (>= 0.9.4.1), stringr (>= 1.0.0), RColorBrewer (>= 1.1-2), DECIPHER (>= 1.16.1), lpSolveAPI (>= 5.5.2.0-17), digest (>= 0.6.9), Hmisc (>= 3.17-4), ape (>= 3.5), BiocGenerics (>= 0.16.1), S4Vectors (>= 0.8.11), foreach (>= 1.4.3), magrittr (>= 1.5), distr (>= 2.6), distrEx (>= 2.6), fitdistrplus (>= 1.0-7), uniqtag (>= 1.0), openxlsx (>= 4.0.17), grid (>= 3.1.0), grDevices (>= 3.1.0), stats (>= 3.1.0), utils (>= 3.1.0), methods (>= 3.1.0) Suggests: testthat (>= 1.0.2), knitr (>= 1.13), rmarkdown (>= 1.0), devtools (>= 1.12.0), doParallel (>= 1.0.10), pander (>= 0.6.0), learnr (>= 0.9) License: GPL-2 MD5sum: 9ed5c077b4649d787db87f1137d043e2 NeedsCompilation: no Package: openPrimeRui Version: 1.20.0 Depends: R (>= 4.0.0), openPrimeR (>= 0.99.0) Imports: shiny (>= 1.0.2), shinyjs (>= 0.9), shinyBS (>= 0.61), DT (>= 0.2), rmarkdown (>= 1.0) Suggests: knitr (>= 1.13) License: GPL-2 MD5sum: dcc8449cf04486baf4aaaa9363b6776a NeedsCompilation: no Package: OpenStats Version: 1.10.0 Depends: nlme Imports: MASS, jsonlite, Hmisc, methods, knitr, AICcmodavg, car, rlist, summarytools, graphics, stats, utils Suggests: rmarkdown License: GPL (>= 2) MD5sum: 9ccb5135a70de805eb20c3e4bfddc688 NeedsCompilation: no Package: oposSOM Version: 2.16.0 Depends: R (>= 4.0.0), igraph (>= 1.0.0) Imports: fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt, Biobase, RcppParallel, Rcpp, methods, graph, XML, png, RCurl LinkingTo: RcppParallel, Rcpp License: GPL (>= 2) MD5sum: 81f1d624eafb33d39bd74485e5d2a9ea NeedsCompilation: yes Package: oppar Version: 1.26.0 Depends: R (>= 3.3) Imports: Biobase, methods, GSEABase, GSVA Suggests: knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel License: GPL-2 MD5sum: 631743cc1331c4d9f0d2220f106b9cc1 NeedsCompilation: yes Package: oppti Version: 1.12.0 Depends: R (>= 3.5) Imports: limma, stats, reshape, ggplot2, grDevices, RColorBrewer, pheatmap, knitr, methods, devtools, parallelDist, Suggests: markdown License: MIT MD5sum: 29a90b1b288a8d0d99e5772a4190bcf3 NeedsCompilation: no Package: optimalFlow Version: 1.10.0 Depends: dplyr, optimalFlowData, rlang (>= 0.4.0) Imports: transport, parallel, Rfast, robustbase, dbscan, randomForest, foreach, graphics, doParallel, stats, flowMeans, rgl, ellipse Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: 8bef2f2bc99a4eb24d914c9baa2f982e NeedsCompilation: no Package: OPWeight Version: 1.20.0 Depends: R (>= 3.4.0), Imports: graphics, qvalue, MASS, tibble, stats, Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat License: Artistic-2.0 MD5sum: ad21b94e92be77f99ff32c3c9eb2e325 NeedsCompilation: no Package: OrderedList Version: 1.70.0 Depends: R (>= 3.6.1), Biobase, twilight Imports: methods License: GPL (>= 2) MD5sum: c468e5a04913b6e2bdbc069b12d14e81 NeedsCompilation: no Package: ORFhunteR Version: 1.6.0 Depends: Biostrings, rtracklayer, Peptides Imports: Rcpp (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg38, data.table, stringr, randomForest, xfun, stats, utils, parallel, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: c5466308777bb491eed8747f444a523f NeedsCompilation: yes Package: ORFik Version: 1.18.2 Depends: R (>= 3.6.0), IRanges (>= 2.17.1), GenomicRanges (>= 1.35.1), GenomicAlignments (>= 1.19.0) Imports: AnnotationDbi (>= 1.45.0), Biostrings (>= 2.51.1), biomaRt, biomartr, BiocGenerics (>= 0.29.1), BiocParallel (>= 1.19.0), BSgenome, cowplot (>= 1.0.0), data.table (>= 1.11.8), DESeq2 (>= 1.24.0), fst (>= 0.9.2), GenomeInfoDb (>= 1.15.5), GenomicFeatures (>= 1.31.10), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), httr (>= 1.3.0), jsonlite, methods (>= 3.6.0), R.utils, Rcpp (>= 1.0.0), Rsamtools (>= 1.35.0), rtracklayer (>= 1.43.0), stats, SummarizedExperiment (>= 1.14.0), S4Vectors (>= 0.21.3), tools, utils, xml2 (>= 1.2.0) LinkingTo: Rcpp Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: e827871a085a52b6921f0fbff2417045 NeedsCompilation: yes Package: Organism.dplyr Version: 1.26.0 Depends: R (>= 3.4), dplyr (>= 0.7.0), AnnotationFilter (>= 1.1.3) Imports: RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges, GenomicFeatures, AnnotationDbi, rlang, methods, tools, utils, BiocFileCache, DBI, dbplyr, tibble Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, BiocStyle, ggplot2 License: Artistic-2.0 MD5sum: e73900859791a888fc08ca8dd5b80c9e NeedsCompilation: no Package: OrganismDbi Version: 1.40.0 Depends: R (>= 2.14.0), methods, BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.39.4) Imports: Biobase, BiocManager, GenomicRanges (>= 1.31.13), graph, IRanges, RBGL, DBI, S4Vectors (>= 0.9.25), stats Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB License: Artistic-2.0 MD5sum: 8f9943ec3d92a011fc16d7595fad7391 NeedsCompilation: no Package: orthogene Version: 1.4.2 Depends: R (>= 4.1) Imports: dplyr, methods, stats, utils, Matrix, jsonlite, homologene, gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr, patchwork, DelayedArray, grr, repmis, ggtree, tools Suggests: rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB License: GPL-3 MD5sum: 9e10c4beaa2e00e6d3cfe497f31736a3 NeedsCompilation: no Package: OSAT Version: 1.46.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 MD5sum: 8cfa6c8bf4efb64ca8801d9afdda2acd NeedsCompilation: no Package: Oscope Version: 1.28.0 Depends: EBSeq, cluster, testthat, BiocParallel Suggests: BiocStyle License: Artistic-2.0 MD5sum: b029ef5797f581df21a82d730467099e NeedsCompilation: no Package: OTUbase Version: 1.48.0 Depends: R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>= 1.23.15), Biobase, vegan Imports: Biostrings License: Artistic-2.0 MD5sum: a2a6420ab5fef742a272ba845c2404cd NeedsCompilation: no Package: OUTRIDER Version: 1.16.3 Depends: R (>= 3.6), BiocParallel, GenomicFeatures, SummarizedExperiment, data.table, methods Imports: BBmisc, BiocGenerics, DESeq2 (>= 1.16.1), generics, GenomicRanges, ggplot2, grDevices, heatmaply, pheatmap, graphics, IRanges, matrixStats, plotly, plyr, pcaMethods, PRROC, RColorBrewer, reshape2, S4Vectors, scales, splines, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr License: MIT + file LICENSE MD5sum: c1022a732b92312ef6d118e9a26939b4 NeedsCompilation: yes Package: OVESEG Version: 1.14.0 Depends: R (>= 3.6) Imports: stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales License: GPL-2 MD5sum: cec3b974f9dea1da0815dcb4638741f4 NeedsCompilation: yes Package: PAA Version: 1.32.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.6) Imports: e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR, sva LinkingTo: Rcpp Suggests: BiocStyle, RUnit, BiocGenerics, vsn License: BSD_3_clause + file LICENSE MD5sum: d19918868939513b5e7fef5d822b6fac NeedsCompilation: yes Package: packFinder Version: 1.10.0 Depends: R (>= 4.1.0) Imports: Biostrings, GenomicRanges, kmer, ape, methods, IRanges, S4Vectors Suggests: biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle License: GPL-2 MD5sum: b55b4991cf92e3ea22e8fd04dfb1a9ab NeedsCompilation: no Package: padma Version: 1.8.0 Depends: R (>= 4.1.0), SummarizedExperiment, S4Vectors Imports: FactoMineR, MultiAssayExperiment, methods, graphics, stats, utils Suggests: testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot License: GPL (>= 3) MD5sum: 26e4209effc63d9a2a5ae6a59a17acb4 NeedsCompilation: no Package: PADOG Version: 1.40.0 Depends: R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase Imports: limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db, hgu133a.db, KEGGREST, nlme Suggests: doParallel, parallel License: GPL (>= 2) MD5sum: 6e585902b1277b95d355f4c274afd9c6 NeedsCompilation: no Package: pageRank Version: 1.8.0 Depends: R (>= 4.0) Imports: GenomicRanges, igraph, motifmatchr, stats, utils, grDevices, graphics Suggests: bcellViper, BSgenome.Hsapiens.UCSC.hg19, JASPAR2018, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, TFBSTools, GenomicFeatures, annotate License: GPL-2 MD5sum: 4a9dc633ec19c8f896b45e589bbbca70 NeedsCompilation: no Package: PAIRADISE Version: 1.14.0 Depends: R (>= 3.6), nloptr Imports: SummarizedExperiment, S4Vectors, stats, methods, abind, BiocParallel Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 1ee7761d6c5486a5f99ddf26c85f7e17 NeedsCompilation: no Package: paircompviz Version: 1.36.0 Depends: R (>= 2.10), Rgraphviz Imports: Rgraphviz Suggests: multcomp, reshape, rpart, plyr, xtable License: GPL (>= 3.0) MD5sum: 4e547653ab22b2bd5fb0e30056d5283c NeedsCompilation: no Package: pairkat Version: 1.4.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, KEGGREST, igraph, data.table, methods, stats, magrittr, CompQuadForm, tibble Suggests: rmarkdown, knitr, BiocStyle, dplyr License: GPL-3 MD5sum: 784ddd758db00fd278bf53f4c173ce9d NeedsCompilation: no Package: pandaR Version: 1.30.0 Depends: R (>= 3.0.0), methods, Biobase, BiocGenerics, Imports: matrixStats, igraph, ggplot2, grid, reshape, plyr, RUnit, hexbin Suggests: knitr, rmarkdown License: GPL-2 MD5sum: df61a51a0c6376703322d922fc63538e NeedsCompilation: no Package: panelcn.mops Version: 1.20.0 Depends: R (>= 3.5.0), cn.mops, methods, utils, stats, graphics Imports: GenomicRanges, Rsamtools, IRanges, S4Vectors, GenomeInfoDb, grDevices Suggests: knitr, rmarkdown, RUnit, BiocGenerics License: LGPL (>= 2.0) MD5sum: 795516c0f78034bea1c1b7780185f7d3 NeedsCompilation: no Package: PanomiR Version: 1.2.0 Depends: R (>= 4.2.0) Imports: clusterProfiler, dplyr, forcats, GSEABase, igraph, limma, metap, org.Hs.eg.db, parallel, preprocessCore, RColorBrewer, rlang, tibble, withr, utils Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 6a42f1f253aa2fd2f89b095f513a97a0 NeedsCompilation: no Package: panp Version: 1.68.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) Imports: Biobase, methods, stats, utils Suggests: gcrma License: GPL (>= 2) MD5sum: 019428c38c81cf30c084bc931667e016 NeedsCompilation: no Package: PANR Version: 1.44.0 Depends: R (>= 2.14), igraph Imports: graphics, grDevices, MASS, methods, pvclust, stats, utils, RedeR Suggests: snow License: Artistic-2.0 MD5sum: 32dc6542d3abc00c0a41fa46d8ae6052 NeedsCompilation: no Package: PanViz Version: 1.0.0 Depends: R (>= 4.2.0) Imports: tidyr, stringr, dplyr, tibble, magrittr, futile.logger, utils, easycsv, rentrez, igraph, RColorBrewer, data.table, colorspace, grDevices, rlang, methods Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, networkD3, License: Artistic-2.0 MD5sum: 6a5c362f0a72a6abf32510aef77b68d8 NeedsCompilation: no Package: pareg Version: 1.2.0 Depends: R (>= 4.2), tensorflow (>= 2.2.0), tfprobability (>= 0.10.0) Imports: stats, tidyr, purrr, furrr, tibble, glue, tidygraph, igraph, proxy, dplyr, magrittr, ggplot2, ggraph, rlang, progress, Matrix, matrixLaplacian, keras, nloptr, shadowtext, methods, DOSE, stringr, reticulate Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, devtools, plotROC, PRROC, mgsa, topGO, msigdbr, betareg, fgsea, ComplexHeatmap, GGally, ggsignif, circlize, enrichplot, ggnewscale, tidyverse, cowplot, ggfittext License: GPL-3 MD5sum: ca1fc7821f8bffdcb39136a9b46cbff5 NeedsCompilation: no Package: parglms Version: 1.30.0 Depends: methods Imports: BiocGenerics, BatchJobs, foreach, doParallel Suggests: RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges, gwascat, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 55bbe9f3d2b9406cb3083f82b5224ac6 NeedsCompilation: no Package: parody Version: 1.56.0 Depends: R (>= 3.5.0), tools, utils Suggests: knitr, BiocStyle, testthat, rmarkdown License: Artistic-2.0 MD5sum: 12692ac0d5c1eb01e6ecc67cdd631f81 NeedsCompilation: no Package: PAST Version: 1.14.0 Depends: R (>= 4.0) Imports: stats, utils, dplyr, rlang, iterators, parallel, foreach, doParallel, qvalue, rtracklayer, ggplot2, GenomicRanges, S4Vectors Suggests: knitr, rmarkdown License: GPL (>= 3) + file LICENSE MD5sum: 20b5c250a365a417233dcb3ebff43899 NeedsCompilation: no Package: Path2PPI Version: 1.28.0 Depends: R (>= 3.2.1), igraph (>= 1.0.1), methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle License: GPL (>= 2) MD5sum: ae69e228709427ac44cedaefabfb9e41 NeedsCompilation: no Package: pathifier Version: 1.36.0 Imports: R.oo, princurve (>= 2.0.4) License: Artistic-1.0 MD5sum: f1c80d82787aab53a20a3a6ebf096df8 NeedsCompilation: no Package: PathNet Version: 1.38.0 Suggests: PathNetData, RUnit, BiocGenerics License: GPL-3 MD5sum: d338f895d806194c645215682f11b50f NeedsCompilation: no Package: PathoStat Version: 1.24.0 Depends: R (>= 3.5) Imports: limma, corpcor,matrixStats, reshape2, scales, ggplot2, rentrez, DT, tidyr, plyr, dplyr, phyloseq, shiny, stats, methods, XML, graphics, utils, BiocStyle, edgeR, DESeq2, ComplexHeatmap, plotly, webshot, vegan, shinyjs, glmnet, gmodels, ROCR, RColorBrewer, knitr, devtools, ape Suggests: rmarkdown, testthat License: GPL (>= 2) MD5sum: ef2d509dad70cad92a110d8b536330b8 NeedsCompilation: no Package: pathRender Version: 1.66.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods, stats4 Suggests: ALL, hgu95av2.db License: LGPL MD5sum: f6beb0530c7f499593d74d907b479f22 NeedsCompilation: no Package: pathVar Version: 1.28.0 Depends: R (>= 3.3.0), methods, ggplot2, gridExtra Imports: EMT, mclust, Matching, data.table, stats, grDevices, graphics, utils License: LGPL (>= 2.0) MD5sum: 81a7ce01202ec4e3bc5c18c0cbc3cabf NeedsCompilation: no Package: pathview Version: 1.38.0 Depends: R (>= 3.5.0) Imports: KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) MD5sum: 74fb173381014b8c5d4cdbdbdd1e2e21 NeedsCompilation: no Package: pathwayPCA Version: 1.14.0 Depends: R (>= 3.1) Imports: lars, methods, parallel, stats, survival, utils Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse License: GPL-3 MD5sum: b530975ed7189e68cdf9e954a17c71da NeedsCompilation: no Package: paxtoolsr Version: 1.32.0 Depends: R (>= 3.2), rJava (>= 0.9-8), methods, XML Imports: utils, httr, igraph, plyr, rjson, R.utils, jsonlite, readr, rappdirs Suggests: testthat, knitr, BiocStyle, formatR, rmarkdown, RColorBrewer, foreach, doSNOW, parallel, org.Hs.eg.db, clusterProfiler License: LGPL-3 MD5sum: 1e4277e9841c1b115e60072c9625584a NeedsCompilation: no Package: pcaExplorer Version: 2.24.0 Imports: DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, genefilter, ggplot2 (>= 2.0.0), heatmaply, plotly, scales, NMF, plyr, topGO, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, ggrepel, DT, shinyAce, threejs, biomaRt, pheatmap, knitr, rmarkdown, base64enc, tidyr, grDevices, methods Suggests: testthat, BiocStyle, airway, org.Hs.eg.db, htmltools License: MIT + file LICENSE MD5sum: 4ab5a9e0980f63a76b400f2986503c61 NeedsCompilation: no Package: pcaMethods Version: 1.90.0 Depends: Biobase, methods Imports: BiocGenerics, Rcpp (>= 0.11.3), MASS LinkingTo: Rcpp Suggests: matrixStats, lattice, ggplot2 License: GPL (>= 3) MD5sum: 700a3beac1bd134bf8817b07f12cc64a NeedsCompilation: yes Package: PCAN Version: 1.26.0 Depends: R (>= 3.3), BiocParallel Imports: grDevices, stats Suggests: BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb License: CC BY-NC-ND 4.0 MD5sum: 53712e79df7e0535f804722a7da781bf NeedsCompilation: no Package: PCAtools Version: 2.10.0 Depends: ggplot2, ggrepel Imports: lattice, grDevices, cowplot, methods, reshape2, stats, Matrix, DelayedMatrixStats, DelayedArray, BiocSingular, BiocParallel, Rcpp, dqrng LinkingTo: Rcpp, beachmat, BH, dqrng Suggests: testthat, scran, BiocGenerics, knitr, Biobase, GEOquery, hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2, airway, org.Hs.eg.db, magrittr, rmarkdown License: GPL-3 MD5sum: 946d754922b2d19569ad834cd3ba4460 NeedsCompilation: yes Package: pcxn Version: 2.20.0 Depends: R (>= 3.4), pcxnData Imports: methods, grDevices, utils, pheatmap Suggests: igraph, annotate, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 29841d9469ed9a99e0a298e4da5f1c67 NeedsCompilation: no Package: PDATK Version: 1.6.0 Depends: R (>= 4.1), SummarizedExperiment Imports: data.table, MultiAssayExperiment, ConsensusClusterPlus, igraph, ggplotify, matrixStats, RColorBrewer, clusterRepro, CoreGx, caret, survminer, methods, S4Vectors, BiocGenerics, survival, stats, plyr, dplyr, MatrixGenerics, BiocParallel, rlang, piano, scales, survcomp, genefu, ggplot2, switchBox, reportROC, pROC, verification, utils Suggests: testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr, HDF5Array License: MIT + file LICENSE MD5sum: 6dc56d7f10125083b10b352ac47ff6ab NeedsCompilation: no Package: pdInfoBuilder Version: 1.62.0 Depends: R (>= 3.2.0), methods, Biobase (>= 2.27.3), RSQLite (>= 1.0.0), affxparser (>= 1.39.4), oligo (>= 1.31.5) Imports: Biostrings (>= 2.35.12), BiocGenerics (>= 0.13.11), DBI (>= 0.3.1), IRanges (>= 2.1.43), oligoClasses (>= 1.29.6), S4Vectors (>= 0.5.22) License: Artistic-2.0 MD5sum: 9da5c6b724867d8bd3c1d1576ccf2d6a NeedsCompilation: yes Package: PeacoQC Version: 1.8.0 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, flowCore, flowWorkspace, ggplot2, grDevices, grid, gridExtra, methods, plyr, stats, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 3) MD5sum: 6c5052ec6bf9ae07b5163f282eb04d41 NeedsCompilation: no Package: peakPantheR Version: 1.12.2 Depends: R (>= 4.2) Imports: foreach (>= 1.4.4), doParallel (>= 1.0.11), ggplot2 (>= 3.3.0), gridExtra (>= 2.3), MSnbase (>= 2.4.0), mzR (>= 2.12.0), stringr (>= 1.2.0), methods (>= 3.4.0), XML (>= 3.98.1.10), minpack.lm (>= 1.2.1), scales(>= 0.5.0), shiny (>= 1.0.5), bslib, shinycssloaders (>= 1.0.0), DT (>= 0.15), pracma (>= 2.2.3), utils, lubridate Suggests: testthat, devtools, faahKO, msdata, knitr, rmarkdown, pander, BiocStyle License: GPL-3 MD5sum: 8d0b0922281818b7f362ef302bc385e6 NeedsCompilation: no Package: PECA Version: 1.34.0 Depends: R (>= 3.3) Imports: ROTS, limma, affy, genefilter, preprocessCore, aroma.affymetrix, aroma.core Suggests: SpikeIn License: GPL (>= 2) MD5sum: b753e2409744304c760fcd3ef6d08fe3 NeedsCompilation: no Package: peco Version: 1.10.0 Depends: R (>= 3.5.0) Imports: assertthat, circular, conicfit, doParallel, foreach, genlasso (>= 1.4), graphics, methods, parallel, scater, SingleCellExperiment, SummarizedExperiment, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 3) MD5sum: 96a70530ba2ff34c227b310522a6e28a NeedsCompilation: no Package: pengls Version: 1.4.0 Depends: R (>= 4.2.0) Imports: glmnet, nlme, stats, BiocParallel Suggests: knitr,rmarkdown,testthat License: GPL-2 MD5sum: e799feb5d1bdd469f5bd727d6d65f463 NeedsCompilation: no Package: PepsNMR Version: 1.16.0 Depends: R (>= 3.6) Imports: Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2, methods, graphics, stats Suggests: knitr, markdown, rmarkdown, BiocStyle, PepsNMRData License: GPL-2 | file LICENSE MD5sum: fe20af94cf4dce41b0c409b7d90b4721 NeedsCompilation: no Package: pepStat Version: 1.32.0 Depends: R (>= 3.0.0), Biobase, IRanges Imports: limma, fields, GenomicRanges, ggplot2, plyr, tools, methods, data.table Suggests: pepDat, Pviz, knitr, shiny License: Artistic-2.0 MD5sum: 38910e377dd84136891dc8768dbecf7e NeedsCompilation: no Package: pepXMLTab Version: 1.32.0 Depends: R (>= 3.0.1) Imports: XML(>= 3.98-1.1) Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 2f30f83653f1f245c06f9f31e53ad946 NeedsCompilation: no Package: PERFect Version: 1.12.0 Depends: R (>= 3.6.0), sn (>= 1.5.2) Imports: ggplot2 (>= 3.0.0), phyloseq (>= 1.28.0), zoo (>= 1.8.3), psych (>= 1.8.4), stats (>= 3.6.0), Matrix (>= 1.2.14), fitdistrplus (>= 1.0.12), parallel (>= 3.6.0) Suggests: knitr, rmarkdown, kableExtra, ggpubr License: Artistic-2.0 MD5sum: 9cfb9d69dc1a083cd026134cfd3b2e21 NeedsCompilation: no Package: periodicDNA Version: 1.8.0 Depends: R (>= 4.0), Biostrings, GenomicRanges, IRanges, BSgenome, BiocParallel Imports: S4Vectors, rtracklayer, stats, GenomeInfoDb, magrittr, zoo, ggplot2, methods, parallel, cowplot Suggests: BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr, knitr, rmarkdown, pkgdown License: GPL-3 + file LICENSE MD5sum: f2492ea9bcd450e9142dee76875bb75f NeedsCompilation: no Package: PFP Version: 1.6.0 Depends: R (>= 4.0) Imports: graph, igraph, KEGGgraph, clusterProfiler, ggplot2, plyr, tidyr, magrittr, stats, methods, utils Suggests: knitr, testthat, rmarkdown, org.Hs.eg.db License: GPL-2 MD5sum: 4c195508b80cdd6e2d182965a32dd8d8 NeedsCompilation: no Package: pgca Version: 1.22.0 Imports: utils, stats Suggests: knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: a5ea5002df59d9dded6354cf769c1a6b NeedsCompilation: no Package: phantasus Version: 1.18.4 Depends: R (>= 3.5) Imports: ggplot2, protolite, Biobase, GEOquery, Rook, htmltools, httpuv, jsonlite, limma, opencpu, assertthat, methods, httr, rhdf5, utils, parallel, stringr, fgsea (>= 1.9.4), svglite, gtable, stats, Matrix, pheatmap, scales, ccaPP, grid, grDevices, AnnotationDbi, DESeq2, data.table, curl Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: c542ef259ff4029a0a4f06e289ddddd5 NeedsCompilation: no Package: PharmacoGx Version: 3.2.0 Depends: R (>= 3.6), CoreGx Imports: BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, magicaxis, RColorBrewer, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, checkmate, boot, coop LinkingTo: Rcpp Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle License: GPL (>= 3) MD5sum: d48ca1013ad8dbe88df73174ad0a2ff2 NeedsCompilation: yes Package: phemd Version: 1.14.1 Depends: R (>= 3.5), monocle, Seurat Imports: SingleCellExperiment, RColorBrewer, igraph, transport, pracma, cluster, Rtsne, destiny, RANN, ggplot2, maptree, pheatmap, scatterplot3d, VGAM, methods, grDevices, graphics, stats, utils, cowplot, S4Vectors, BiocGenerics, SummarizedExperiment, Biobase, phateR, reticulate Suggests: knitr License: GPL-2 MD5sum: 2f8a7d63e9747a7b2f8f099d1009ce00 NeedsCompilation: no Package: PhenoGeneRanker Version: 1.6.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 International License MD5sum: b5b666ffec19642d6d1a2f7f77a56b82 NeedsCompilation: no Package: phenomis Version: 1.0.2 Depends: SummarizedExperiment Imports: Biobase, biodb, biodbChebi, data.table, futile.logger, ggplot2, ggrepel, graphics, grDevices, grid, htmlwidgets, igraph, limma, methods, MultiAssayExperiment, MultiDataSet, PMCMRplus, plotly, ranger, RColorBrewer, ropls, stats, tibble, tidyr, utils, VennDiagram Suggests: BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4, rmarkdown, testthat License: CeCILL MD5sum: 1490b92264a0a57b473e57cc8409f1f4 NeedsCompilation: no Package: phenopath Version: 1.22.0 Imports: Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr, tibble, ggplot2, tidyr LinkingTo: Rcpp Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment License: Apache License (== 2.0) MD5sum: 88ebeb09839decbce45974019138fad2 NeedsCompilation: yes Package: phenoTest Version: 1.46.0 Depends: R (>= 3.6.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2, Hmisc Imports: survival, limma, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, hgu133a.db, ellipse Suggests: GSEABase, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) MD5sum: 51930f0e486e33a43f414dd8c7b9a312 NeedsCompilation: no Package: PhenStat Version: 2.34.0 Depends: R (>= 3.5.0) Imports: SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf, knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4, graphics, grDevices, utils, stats Suggests: RUnit, BiocGenerics License: file LICENSE MD5sum: 7dced586e94fcf13cacbfd0f581fd56d NeedsCompilation: no Package: philr Version: 1.24.0 Imports: ape, phangorn, tidyr, ggplot2, ggtree, methods Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia License: GPL-3 MD5sum: 988e7af713c22b59fc49b9eb7d73d14a NeedsCompilation: no Package: PhIPData Version: 1.6.0 Depends: R (>= 4.1.0), SummarizedExperiment (>= 1.3.81) Imports: BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors, edgeR, cli, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr License: MIT + file LICENSE MD5sum: fa207d90ab4338e50b62dec150973f27 NeedsCompilation: no Package: phosphonormalizer Version: 1.22.0 Depends: R (>= 4.0) Imports: plyr, stats, graphics, matrixStats, methods Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) MD5sum: 6ec7cdb7b0592ce2e4c249e76eeea5c0 NeedsCompilation: no Package: PhosR Version: 1.8.0 Depends: R (>= 4.1.0) Imports: ruv, e1071, dendextend, limma, pcaMethods, stats, RColorBrewer, circlize, dplyr, igraph, pheatmap, preprocessCore, tidyr, rlang, graphics, grDevices, utils, SummarizedExperiment, methods, S4Vectors, BiocGenerics, ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate License: GPL-3 + file LICENSE MD5sum: 316c8ece1f21947509b638a657eea0eb NeedsCompilation: no Package: PhyloProfile Version: 1.12.6 Depends: R (>= 4.2.0) Imports: ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, DT, energy, ExperimentHub, ggplot2, gridExtra, pbapply, RColorBrewer, RCurl, shiny, shinyBS, shinyFiles, shinyjs, OmaDB, plyr, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 914a7c7fc33188eb0eff65587c3981bf NeedsCompilation: no Package: phyloseq Version: 1.42.0 Depends: R (>= 3.3.0) Imports: ade4 (>= 1.7-4), ape (>= 5.0), Biobase (>= 2.36.2), BiocGenerics (>= 0.22.0), biomformat (>= 1.0.0), Biostrings (>= 2.40.0), cluster (>= 2.0.4), data.table (>= 1.10.4), foreach (>= 1.4.3), ggplot2 (>= 2.1.0), igraph (>= 1.0.1), methods (>= 3.3.0), multtest (>= 2.28.0), plyr (>= 1.8.3), reshape2 (>= 1.4.1), scales (>= 0.4.0), vegan (>= 2.5) Suggests: BiocStyle (>= 2.4), DESeq2 (>= 1.16.1), genefilter (>= 1.58), knitr (>= 1.16), magrittr (>= 1.5), metagenomeSeq (>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2) Enhances: doParallel (>= 1.0.10) License: AGPL-3 MD5sum: edf40c9718a0242aec1731026fa9c610 NeedsCompilation: no Package: Pi Version: 2.10.0 Depends: igraph, dnet, ggplot2, graphics Imports: Matrix, GenomicRanges, GenomeInfoDb, supraHex, scales, grDevices, ggrepel, ROCR, randomForest, glmnet, lattice, caret, plot3D, stats, methods, MASS, IRanges, BiocGenerics, dplyr, tidyr, ggnetwork, osfr, RCircos, purrr, readr, tibble Suggests: foreach, doParallel, BiocStyle, knitr, rmarkdown, png, GGally, gridExtra, ggforce, fgsea, RColorBrewer, ggpubr, rtracklayer, ggbio, Gviz, data.tree, jsonlite License: GPL-3 MD5sum: bb7b0d9d7b90347c7459a00e0ca2eb9a NeedsCompilation: no Package: piano Version: 2.14.0 Depends: R (>= 3.5) Imports: BiocGenerics, Biobase, gplots, igraph, relations, marray, fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard, visNetwork, scales, grDevices, graphics, stats, utils, methods Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 56f7a2c1893fa5af9bf5f5ba40b20fb6 NeedsCompilation: no Package: pickgene Version: 1.70.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: 4aea3a16f350f432867f032e1700ec2e NeedsCompilation: no Package: PICS Version: 2.42.0 Depends: R (>= 3.0.0) Imports: utils, stats, graphics, grDevices, methods, IRanges, GenomicRanges, Rsamtools, GenomicAlignments Suggests: rtracklayer, parallel, knitr License: Artistic-2.0 MD5sum: 7430d3f4c1ba2ed9e655f8fc3caa0fdf NeedsCompilation: yes Package: Pigengene Version: 1.24.0 Depends: R (>= 4.0.3), graph, BiocStyle (>= 2.18.1) Imports: bnlearn (>= 4.7), C50 (>= 0.1.2), MASS, matrixStats, partykit, Rgraphviz, WGCNA, GO.db, impute, preprocessCore, grDevices, graphics, stats, utils, parallel, pheatmap (>= 1.0.8), dplyr, gdata, clusterProfiler, ReactomePA, ggplot2, openxlsx, DBI, DOSE Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>= 2.30.0), knitr, AnnotationDbi, energy License: GPL (>= 2) MD5sum: 1b24f875454e673dbe3b6be48985c978 NeedsCompilation: no Package: PING Version: 2.42.0 Depends: R(>= 3.5.0) Imports: methods, PICS, graphics, grDevices, stats, Gviz, fda, BSgenome, stats4, BiocGenerics, IRanges, GenomicRanges, S4Vectors Suggests: parallel, ShortRead, rtracklayer License: Artistic-2.0 MD5sum: fb4ec5041e863c1038b8ba014992ec12 NeedsCompilation: yes Package: pipeComp Version: 1.8.0 Depends: R (>= 4.1) Imports: BiocParallel, S4Vectors, ComplexHeatmap, SingleCellExperiment, SummarizedExperiment, Seurat, matrixStats, Matrix, cluster, aricode, methods, utils, dplyr, grid, scales, scran, viridisLite, clue, randomcoloR, ggplot2, cowplot, intrinsicDimension, scater, knitr, reshape2, stats, Rtsne, uwot, circlize, RColorBrewer Suggests: BiocStyle, rmarkdown License: GPL MD5sum: b6913a4fdd99bc7d42ccd1b617b2bf2a NeedsCompilation: no Package: pipeFrame Version: 1.14.0 Depends: R (>= 4.0.0), Imports: BSgenome, digest, visNetwork, magrittr, methods, Biostrings, GenomeInfoDb, parallel, stats, utils, rmarkdown Suggests: BiocManager, knitr, rtracklayer, testthat License: GPL-3 MD5sum: 2555bb338c143020a5268ce24dee123a NeedsCompilation: no Package: pkgDepTools Version: 1.63.0 Depends: methods, graph, RBGL Imports: graph, RBGL Suggests: Biobase, Rgraphviz, RCurl, BiocManager License: GPL-2 MD5sum: 920edaddf79dcd16bd4f2a2ca6e7c72b NeedsCompilation: no Package: planet Version: 1.6.0 Depends: R (>= 4.0) Imports: methods, tibble, magrittr, dplyr Suggests: ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr, rmarkdown License: GPL-2 MD5sum: 55e48dd368edd0bb33733605ffc4bed8 NeedsCompilation: no Package: plethy Version: 1.36.0 Depends: R (>= 3.1.0), methods, DBI (>= 0.5-1), RSQLite (>= 1.1), BiocGenerics, S4Vectors Imports: Streamer, IRanges, reshape2, plyr, RColorBrewer,ggplot2, Biobase Suggests: RUnit, BiocStyle License: GPL-3 MD5sum: 449d5f82b30430a259505be9cecae231 NeedsCompilation: no Package: plgem Version: 1.70.0 Depends: R (>= 2.10) Imports: utils, Biobase (>= 2.5.5), MASS, methods License: GPL-2 MD5sum: b6743e303cbb3acbb4e764a0991f490f NeedsCompilation: no Package: plier Version: 1.68.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) MD5sum: e3fcc02d9b478c31ea494c34a81447b2 NeedsCompilation: yes Package: PloGO2 Version: 1.10.0 Depends: R (>= 4.0), GO.db, GOstats Imports: lattice, httr, openxlsx, xtable License: GPL-2 MD5sum: 35d47bf501fc13ea48bac0ba216d1f4e NeedsCompilation: no Package: plotgardener Version: 1.4.2 Depends: R (>= 4.1.0) Imports: curl, data.table, dplyr, grDevices, grid, ggplotify, IRanges, methods, plyranges, purrr, Rcpp, RColorBrewer, rlang, stats, strawr, tools, utils LinkingTo: Rcpp Suggests: AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, GenomeInfoDb, GenomicRanges, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene License: MIT + file LICENSE MD5sum: 1e90b16ac8b11e3aabf7fe9a1314c572 NeedsCompilation: yes Package: plotGrouper Version: 1.16.0 Depends: R (>= 3.5) Imports: ggplot2 (>= 3.0.0), dplyr (>= 0.7.6), tidyr (>= 0.2.0), tibble (>= 1.4.2), stringr (>= 1.3.1), readr (>= 1.1.1), readxl (>= 1.1.0), scales (>= 1.0.0), stats, grid, gridExtra (>= 2.3), egg (>= 0.4.0), gtable (>= 0.2.0), ggpubr (>= 0.1.8), shiny (>= 1.1.0), shinythemes (>= 1.1.1), colourpicker (>= 1.0), magrittr (>= 1.5), Hmisc (>= 4.1.1), rlang (>= 0.2.2) Suggests: knitr, htmltools, BiocStyle, rmarkdown, testthat License: GPL-3 MD5sum: 6287474de924766cf7bbf00fde0a1cae NeedsCompilation: no Package: PLPE Version: 1.58.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) MD5sum: 95abd992d420577d056009d4ff143956 NeedsCompilation: no Package: plyranges Version: 1.18.0 Depends: R (>= 3.5), BiocGenerics, IRanges (>= 2.12.0), GenomicRanges (>= 1.28.4) Imports: methods, dplyr, rlang (>= 0.2.0), magrittr, tidyselect (>= 1.0.0), rtracklayer, GenomicAlignments, GenomeInfoDb, Rsamtools, S4Vectors (>= 0.23.10), utils Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 2.1.0), HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, covr, ggplot2 License: Artistic-2.0 MD5sum: 0f987f6850662c460cd5d9785f6b9122 NeedsCompilation: no Package: pmm Version: 1.30.0 Depends: R (>= 2.10) Imports: lme4, splines License: GPL-3 MD5sum: e32231e0857b47f160d73470632206bd NeedsCompilation: no Package: pmp Version: 1.10.0 Depends: R (>= 4.0) Imports: stats, impute, pcaMethods, missForest, ggplot2, methods, SummarizedExperiment, S4Vectors, matrixStats, grDevices, reshape2, utils Suggests: testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra, magick License: GPL-3 MD5sum: fe8eae5ee1b752b11508d83c17ad7550 NeedsCompilation: no Package: PoDCall Version: 1.6.0 Depends: R (>= 4.2) Imports: ggplot2, gridExtra, mclust, diptest, rlist, shiny, DT, LaplacesDemon, purrr, shinyjs, readr, grDevices, stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 5873a3a7cbfe65a0402aed8e7b1cc20a NeedsCompilation: no Package: podkat Version: 1.30.0 Depends: R (>= 3.5.0), methods, Rsamtools (>= 1.99.1), GenomicRanges Imports: Rcpp (>= 0.11.1), parallel, stats, graphics, grDevices, utils, Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges, Biostrings, BSgenome (>= 1.32.0) LinkingTo: Rcpp, Rhtslib (>= 1.15.3) Suggests: BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr License: GPL (>= 2) MD5sum: c7a6518f5940692d915312889811b4b2 NeedsCompilation: yes Package: pogos Version: 1.18.0 Depends: R (>= 3.5.0), rjson (>= 0.2.15), httr (>= 1.3.1) Imports: methods, S4Vectors, utils, shiny, ontoProc, ggplot2, graphics Suggests: knitr, DT, ontologyPlot, testthat, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: a4e1366a8ffe214852f79e2f99c6e596 NeedsCompilation: no Package: polyester Version: 1.34.0 Depends: R (>= 3.0.0) Imports: Biostrings (>= 2.32.0), IRanges, S4Vectors, logspline, limma, zlibbioc Suggests: knitr, ballgown, markdown License: Artistic-2.0 MD5sum: 590c94919c358a4ea6381c2b76f427d7 NeedsCompilation: no Package: POMA Version: 1.8.0 Depends: R (>= 4.0) Imports: broom, caret, ComplexHeatmap, dbscan, dplyr, DESeq2, ggplot2, ggrepel, glasso (>= 1.11), glmnet, impute, limma, magrittr, mixOmics, randomForest, RankProd (>= 3.14), rmarkdown, SummarizedExperiment, tibble, tidyr, uwot, vegan Suggests: BiocStyle, covr, ggraph, knitr, patchwork, plotly, tidyverse, testthat (>= 2.3.2) License: GPL-3 MD5sum: 62f4d7ae06dc971d3ac6cfa99cac45e4 NeedsCompilation: no Package: PoTRA Version: 1.13.0 Depends: R (>= 3.6.0), stats, BiocGenerics, org.Hs.eg.db, igraph, graph, graphite Suggests: BiocStyle, knitr, rmarkdown, colr, metap, repmis License: LGPL MD5sum: 02bf318cec1add1135188fe30a7bbb1d NeedsCompilation: no Package: powerTCR Version: 1.18.0 Imports: cubature, doParallel, evmix, foreach, magrittr, methods, parallel, purrr, stats, truncdist, vegan, VGAM Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: c06a9c5ae01529c0e3d125c3628d3df7 NeedsCompilation: no Package: POWSC Version: 1.6.0 Depends: R (>= 4.1), Biobase, SingleCellExperiment, MAST Imports: pheatmap, ggplot2, RColorBrewer, grDevices, SummarizedExperiment, limma Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-2 MD5sum: a25ab9cad5c3baaebf03860213214377 NeedsCompilation: no Package: ppcseq Version: 1.6.0 Depends: R (>= 4.1.0) Imports: methods, Rcpp (>= 0.12.0), rstan (>= 2.18.1), rstantools (>= 2.0.0), tibble, dplyr, magrittr, purrr, future, furrr, tidyr (>= 0.8.3.9000), lifecycle, ggplot2, foreach, tidybayes, edgeR, benchmarkme, parallel, rlang, stats, utils, graphics LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: knitr, testthat, BiocStyle, rmarkdown License: GPL-3 MD5sum: 26ba8f7f77732973d7cdcd1229cf2b97 NeedsCompilation: yes Package: PPInfer Version: 1.24.2 Depends: biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb, yeastExpData Imports: httr, grDevices, graphics, stats, utils License: Artistic-2.0 MD5sum: 98bd1ba94f206e55440b649211e88db9 NeedsCompilation: no Package: pqsfinder Version: 2.14.1 Depends: R (>= 3.5.0), Biostrings Imports: Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods LinkingTo: Rcpp, BH (>= 1.78.0) Suggests: BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi License: BSD_2_clause + file LICENSE MD5sum: 122f1398e999e70312dd2c8d3f68b77c NeedsCompilation: yes Package: pram Version: 1.14.0 Depends: R (>= 3.6) Imports: methods, BiocParallel, tools, utils, data.table (>= 1.11.8), GenomicAlignments (>= 1.16.0), rtracklayer (>= 1.40.6), BiocGenerics (>= 0.26.0), GenomeInfoDb (>= 1.16.0), GenomicRanges (>= 1.32.0), IRanges (>= 2.14.12), Rsamtools (>= 1.32.3), S4Vectors (>= 0.18.3) Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 3) MD5sum: 24f0079cc585ffd54a5ab028a12633f7 NeedsCompilation: no Package: prebs Version: 1.38.0 Depends: R (>= 2.14.0), GenomicAlignments, affy, RPA Imports: parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges, Biobase, GenomeInfoDb, S4Vectors Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe License: Artistic-2.0 MD5sum: c37527c055244dccf97b8fbd66130bca NeedsCompilation: no Package: preciseTAD Version: 1.8.0 Depends: R (>= 4.1) Imports: S4Vectors, IRanges, GenomicRanges, randomForest, ModelMetrics, e1071, PRROC, pROC, caret, utils, cluster, dbscan, doSNOW, foreach, pbapply, stats, parallel, gtools, rCGH Suggests: knitr, rmarkdown, testthat, BiocCheck, BiocManager, BiocStyle License: MIT + file LICENSE MD5sum: 0aa4053f4198be4b863ff0e9613d16e4 NeedsCompilation: no Package: PREDA Version: 1.44.0 Depends: R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats, methods, annotate Suggests: quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata Enhances: Rmpi, rsprng License: GPL-2 MD5sum: 5859c6d37d24cd88d1dfa5232716db3e NeedsCompilation: no Package: preprocessCore Version: 1.60.2 Imports: stats License: LGPL (>= 2) MD5sum: 803d83c635bc9d859a287ea8e714076a NeedsCompilation: yes Package: primirTSS Version: 1.16.0 Depends: R (>= 3.5.0) Imports: GenomicRanges (>= 1.32.2), S4Vectors (>= 0.18.2), rtracklayer (>= 1.40.3), dplyr (>= 0.7.6), stringr (>= 1.3.1), tidyr (>= 0.8.1), Biostrings (>= 2.48.0), purrr (>= 0.2.5), BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.1), phastCons100way.UCSC.hg38 (>= 3.7.1), GenomicScores (>= 1.4.1), shiny (>= 1.0.5), Gviz (>= 1.24.0), BiocGenerics (>= 0.26.0), IRanges (>= 2.14.10), TFBSTools (>= 1.18.0), JASPAR2018 (>= 1.1.1), tibble (>= 1.4.2), R.utils (>= 2.6.0), stats, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 798bacb57857e819725e01cee1adc693 NeedsCompilation: no Package: PrInCE Version: 1.14.0 Depends: R (>= 3.6.0) Imports: purrr (>= 0.2.4), dplyr (>= 0.7.4), tidyr (>= 0.8.99), forecast (>= 8.2), progress (>= 1.1.2), Hmisc (>= 4.0), naivebayes (>= 0.9.1), robustbase (>= 0.92-7), ranger (>= 0.8.0), LiblineaR (>= 2.10-8), speedglm (>= 0.3-2), tester (>= 0.1.7), magrittr (>= 1.5), Biobase (>= 2.40.0), MSnbase (>= 2.8.3), stats, utils, methods, Rdpack (>= 0.7) Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 6180c413739ff4fe86825d9f5698044a NeedsCompilation: no Package: proActiv Version: 1.8.0 Depends: R (>= 4.0.0) Imports: AnnotationDbi, BiocParallel, data.table, dplyr, DESeq2, IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments, GenomeInfoDb, ggplot2, gplots, graphics, methods, rlang, scales, S4Vectors, SummarizedExperiment, stats, tibble Suggests: testthat, rmarkdown, knitr, Rtsne, gridExtra License: MIT + file LICENSE MD5sum: 0c03533d936a898a6628a06ae53d9788 NeedsCompilation: no Package: proBAMr Version: 1.32.0 Depends: R (>= 3.0.1), IRanges, AnnotationDbi Imports: GenomicRanges, Biostrings, GenomicFeatures, rtracklayer Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 5f9cac892c5059c2d7561865953aaccb NeedsCompilation: no Package: proBatch Version: 1.14.0 Depends: R (>= 3.6) Imports: Biobase, corrplot, dplyr, data.table, ggfortify, ggplot2, grDevices, lazyeval, lubridate, magrittr, pheatmap, preprocessCore, purrr, pvca, RColorBrewer, reshape2, rlang, scales, stats, sva, tidyr, tibble, tools, utils, viridis, wesanderson, WGCNA Suggests: knitr, rmarkdown, devtools, ggpubr, gtable, gridExtra, roxygen2, testthat (>= 2.1.0), spelling License: GPL-3 MD5sum: be52699bbc2cd8ba94c17ca720cc1142 NeedsCompilation: no Package: PROcess Version: 1.74.0 Depends: Icens Imports: graphics, grDevices, Icens, stats, utils License: Artistic-2.0 MD5sum: 781bdf154b8ddf4f5fb5a12d8669fe31 NeedsCompilation: no Package: procoil Version: 2.26.0 Depends: R (>= 3.3.0), kebabs Imports: methods, stats, graphics, S4Vectors, Biostrings, utils Suggests: knitr License: GPL (>= 2) MD5sum: b441b211f5eb973da6a69dbc1744dc5c NeedsCompilation: no Package: proDA Version: 1.12.0 Imports: stats, utils, methods, BiocGenerics, SummarizedExperiment, S4Vectors, extraDistr Suggests: testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr, tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown License: GPL-3 MD5sum: 01b5c145bf64cfacebbfec97b92d659e NeedsCompilation: no Package: proFIA Version: 1.23.0 Depends: R (>= 2.5.0), xcms Imports: stats, graphics, utils, grDevices, methods, pracma, Biobase, minpack.lm, BiocParallel, missForest, ropls Suggests: BiocGenerics, plasFIA, knitr, License: CeCILL MD5sum: 125bb66775833222118ebd1e40a1a0b7 NeedsCompilation: yes Package: profileplyr Version: 1.14.1 Depends: R (>= 3.6), BiocGenerics, SummarizedExperiment Imports: GenomicRanges, stats, soGGi, methods, utils, S4Vectors, R.utils, dplyr, magrittr, tidyr, IRanges, rjson, ChIPseeker,GenomicFeatures,TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene,org.Hs.eg.db,org.Mm.eg.db,rGREAT, pheatmap, ggplot2, EnrichedHeatmap, ComplexHeatmap, grid, circlize, BiocParallel, rtracklayer, GenomeInfoDb, grDevices, rlang, tiff, Rsamtools Suggests: BiocStyle, testthat, knitr, rmarkdown, png, Cairo License: GPL (>= 3) MD5sum: a96b7654cc18aa3ad5bfd22f44ba4ab4 NeedsCompilation: no Package: profileScoreDist Version: 1.26.0 Depends: R(>= 3.3) Imports: Rcpp, BiocGenerics, methods, graphics LinkingTo: Rcpp Suggests: BiocStyle, knitr, MotifDb License: MIT + file LICENSE MD5sum: 1736d929cbb6f3257ba9a33d26c41b5e NeedsCompilation: yes Package: progeny Version: 1.20.0 Depends: R (>= 3.6.0) Imports: Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra, decoupleR, reshape2 Suggests: airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0) License: Apache License (== 2.0) | file LICENSE MD5sum: 8baf46a4ce12dd912ee8a0b922c732c2 NeedsCompilation: no Package: projectR Version: 1.14.0 Imports: methods, cluster, stats, limma, CoGAPS, NMF, ROCR, ggalluvial, RColorBrewer, dplyr, reshape2, viridis, scales, ggplot2 Suggests: BiocStyle, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap License: GPL (== 2) MD5sum: 368115c6fc3d01d73938f1bf4788bfa5 NeedsCompilation: no Package: pRoloc Version: 1.38.2 Depends: R (>= 3.5), MSnbase (>= 1.19.20), MLInterfaces (>= 1.67.10), methods, Rcpp (>= 0.10.3), BiocParallel Imports: stats4, Biobase, mclust (>= 4.3), caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS, knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools, plyr, ggplot2, biomaRt, utils, grDevices, graphics LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.15.3), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape, magick License: GPL-2 MD5sum: 20588072a032f202e9f06090b392f12d NeedsCompilation: yes Package: pRolocGUI Version: 2.8.0 Depends: methods, R (>= 3.1.0), pRoloc (>= 1.27.6), Biobase, MSnbase (>= 2.1.11) Imports: shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics, utils, ggplot2, shinydashboardPlus (>= 2.0.0), colourpicker, shinyhelper, shinyWidgets, shinyjs, colorspace, stats, grDevices, grid, BiocGenerics, shinydashboard Suggests: pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown, testthat (>= 3.0.0) License: GPL-2 MD5sum: 400bff2d87e9ba8dae97dcb9126469ec NeedsCompilation: no Package: PROMISE Version: 1.50.0 Depends: R (>= 3.1.0), Biobase, GSEABase Imports: Biobase, GSEABase, stats License: GPL (>= 2) MD5sum: 49ce20be97f0cc7638cd58cf2b6dba3b NeedsCompilation: no Package: PROPER Version: 1.30.0 Depends: R (>= 3.3) Imports: edgeR Suggests: BiocStyle,DESeq2,DSS,knitr License: GPL MD5sum: 7f36d105300d6e3604e654eb41eb8bce NeedsCompilation: no Package: PROPS Version: 1.20.0 Imports: bnlearn, reshape2, sva, stats, utils, Biobase Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 96a01cb749fdbc3fc36266ab9532263b NeedsCompilation: no Package: Prostar Version: 1.30.7 Depends: R (>= 4.2.0) Imports: DAPAR (>= 1.30.5), DAPARdata (>= 1.28.0), rhandsontable, data.table, shiny, shinyBS, shinyAce, highcharter, htmlwidgets, webshot, shinythemes, later, shinycssloaders, future, promises, shinyjqui, tibble, ggplot2, gplots, shinyjs, vioplot Suggests: BiocStyle, BiocManager, testthat, shinyTree, knitr, colourpicker, gtools, XML, R.utils, RColorBrewer, DT, shinyWidgets, sass, rclipboard License: Artistic-2.0 MD5sum: 7cd4f1914a062176bd49cb06a3ac8434 NeedsCompilation: no Package: proteasy Version: 1.0.0 Depends: R (>= 4.2.0) Imports: data.table, stringr, ensembldb, AnnotationFilter, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, EnsDb.Rnorvegicus.v79, Rcpi, methods, utils Suggests: BiocStyle, knitr, rmarkdown, igraph, ComplexHeatmap, viridis, License: GPL-3 MD5sum: 17acfcc126e9ee9181c801bc5afab88e NeedsCompilation: no Package: proteinProfiles Version: 1.38.0 Depends: R (>= 2.15.2) Imports: graphics, stats Suggests: testthat License: GPL-3 MD5sum: fd0032fb672c3dcd381b9fb59166d4a2 NeedsCompilation: no Package: ProteoDisco Version: 1.4.0 Depends: R (>= 4.1.0), Imports: BiocGenerics (>= 0.38.0), BiocParallel (>= 1.26.0), Biostrings (>= 2.60.1), checkmate (>= 2.0.0), cleaver (>= 1.30.0), dplyr (>= 1.0.6), GenomeInfoDb (>= 1.28.0), GenomicFeatures (>= 1.44.0), GenomicRanges (>= 1.44.0), IRanges (>= 2.26.0), methods (>= 4.1.0), ParallelLogger (>= 2.0.1), plyr (>= 1.8.6), rlang (>= 0.4.11), S4Vectors (>= 0.30.0), tibble (>= 3.1.2), tidyr (>= 1.1.3), VariantAnnotation (>= 1.36.0), XVector (>= 0.32.0), Suggests: AnnotationDbi (>= 1.54.1), BSgenome (>= 1.60.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.3), BiocStyle (>= 2.20.1), DelayedArray (>= 0.18.0), devtools (>= 2.4.2), knitr (>= 1.33), matrixStats (>= 0.59.0), markdown (>= 1.1), org.Hs.eg.db (>= 3.13.0), purrr (>= 0.3.4), RCurl (>= 1.98.1.3), readr (>= 1.4.0), ggplot2 (>= 3.3.5), rmarkdown (>= 2.9), rtracklayer (>= 1.52.0), seqinr (>= 4.2.8), stringr (>= 1.4.0), reshape2 (>= 1.4.4), scales (>= 1.1.1), testthat (>= 3.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2) License: GPL-3 MD5sum: 1cf5531210ad22874467ec57e6dab4a8 NeedsCompilation: no Package: ProteoMM Version: 1.16.0 Depends: R (>= 3.5) Imports: gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats, graphics Suggests: BiocStyle, knitr, rmarkdown License: MIT MD5sum: ab59f87cb72ba500bc72a8ef9d630bb7 NeedsCompilation: no Package: protGear Version: 1.2.0 Depends: R (>= 4.2), dplyr (>= 0.8.0) , limma (>= 3.40.2) ,vsn (>= 3.54.0) Imports: magrittr (>= 1.5) , stats (>= 3.6) , ggplot2 (>= 3.3.0) , tidyr (>= 1.1.3) , data.table (>= 1.14.0), ggpubr (>= 0.4.0), gtools (>= 3.8.2) , tibble (>= 3.1.0) , rmarkdown (>= 2.9) , knitr (>= 1.33), utils (>= 3.6), genefilter (>= 1.74.0), readr (>= 2.0.1) , Biobase (>= 2.52.0), plyr (>= 1.8.6) , Kendall (>= 2.2) , shiny (>= 1.0.0) , purrr (>= 0.3.4), plotly (>= 4.9.0) , MASS (>= 7.3) , htmltools (>= 0.4.0) , flexdashboard (>= 0.5.2) , shinydashboard (>= 0.7.1) , kableExtra (>= 1.3.4), GGally (>= 2.1.2) , pheatmap (>= 1.0.12) , grid(>= 4.1.1), styler (>= 1.6.1) , factoextra (>= 1.0.7) ,FactoMineR (>= 2.4) , rlang (>= 0.4.11), remotes (>= 2.4.0) Suggests: gridExtra (>= 2.3), png (>= 0.1-7) , magick (>= 2.7.3) , ggplotify (>= 0.1.0) , scales (>= 1.1.1) , shinythemes (>= 1.2.0) , shinyjs (>= 2.0.0) , shinyWidgets (>= 0.6.2) , shinycssloaders (>= 1.0.0) , shinyalert (>= 3.0.0) , shinyFiles (>= 0.9.1) , shinyFeedback (>= 0.3.0) License: GPL-3 MD5sum: 1056efb679e5f6629e0f4bbe4bf6752b NeedsCompilation: no Package: ProtGenerics Version: 1.30.0 Depends: methods Suggests: testthat License: Artistic-2.0 MD5sum: 0401af6e41ec629a173a1e8dacb12823 NeedsCompilation: no Package: PSEA Version: 1.32.0 Imports: Biobase, MASS Suggests: BiocStyle License: Artistic-2.0 MD5sum: dc1274dd2db6fce4075de1ee4a52e6da NeedsCompilation: no Package: psichomics Version: 1.24.0 Depends: R (>= 4.0), shiny (>= 1.7.0), shinyBS Imports: AnnotationDbi, AnnotationHub, BiocFileCache, cluster, colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR, fastICA, fastmatch, ggplot2, ggrepel, graphics, grDevices, highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma, pairsD3, plyr, purrr, Rcpp (>= 0.12.14), recount, Rfast, R.utils, reshape2, shinyjs, stringr, stats, SummarizedExperiment, survival, tools, utils, XML, xtable, methods LinkingTo: Rcpp Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling License: MIT + file LICENSE MD5sum: e0b5dd013455ac8afc6b30b9dd965645 NeedsCompilation: yes Package: PSMatch Version: 1.2.0 Depends: S4Vectors Imports: utils, stats, igraph, methods, Matrix, BiocParallel, BiocGenerics, ProtGenerics (>= 1.27.1), QFeatures, MsCoreUtils Suggests: msdata, rpx, mzID, mzR, Spectra, SummarizedExperiment, BiocStyle, rmarkdown, knitr, factoextra, testthat License: Artistic-2.0 MD5sum: d6129bf161baf69afb4dad71ca3a965b NeedsCompilation: no Package: psygenet2r Version: 1.30.0 Depends: R (>= 3.4) Imports: stringr, RCurl, igraph, ggplot2, reshape2, grid, parallel, biomaRt, BgeeDB, topGO, Biobase, labeling, GO.db Suggests: testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 7dcb0f99dcb2623989bccdec5afa4274 NeedsCompilation: no Package: ptairMS Version: 1.6.0 Imports: Biobase, bit64, chron, data.table, doParallel, DT, enviPat, foreach, ggplot2, graphics, grDevices, ggpubr, gridExtra, Hmisc, methods, minpack.lm, MSnbase, parallel, plotly, rhdf5, rlang, Rcpp, shiny, shinyscreenshot, signal, scales, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData, ropls License: GPL-3 MD5sum: b1e96e522b44dbb2f4270e8a93d68288 NeedsCompilation: yes Package: puma Version: 3.40.0 Depends: R (>= 3.2.0), oligo (>= 1.32.0),graphics,grDevices, methods, stats, utils, mclust, oligoClasses Imports: Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses Suggests: pumadata, affydata, snow, limma, ROCR,annotate License: LGPL MD5sum: e76d81a75d32dc58facd4040fd4a9402 NeedsCompilation: yes Package: PureCN Version: 2.4.0 Depends: R (>= 3.5.0), DNAcopy, VariantAnnotation (>= 1.14.1) Imports: GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer, S4Vectors, data.table, grDevices, graphics, stats, utils, SummarizedExperiment, GenomeInfoDb, GenomicFeatures, Rsamtools, Biobase, Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra, futile.logger, VGAM, tools, methods, mclust, rhdf5, Matrix Suggests: BiocParallel, BiocStyle, PSCBS, R.utils, TxDb.Hsapiens.UCSC.hg19.knownGene, copynumber, covr, knitr, optparse, org.Hs.eg.db, jsonlite, markdown, rmarkdown, testthat Enhances: genomicsdb (>= 0.0.3) License: Artistic-2.0 MD5sum: e27dab92290f8bc87a24f45d433893e3 NeedsCompilation: no Package: pvac Version: 1.46.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) MD5sum: a60782744069194b06fca1ad7a0cb0e6 NeedsCompilation: no Package: pvca Version: 1.38.0 Depends: R (>= 2.15.1) Imports: Matrix, Biobase, vsn, stats, lme4 Suggests: golubEsets License: LGPL (>= 2.0) MD5sum: 3e0a756f9bd0beab58434428b1b8f400 NeedsCompilation: no Package: Pviz Version: 1.32.0 Depends: R(>= 3.0.0), Gviz(>= 1.7.10) Imports: biovizBase, Biostrings, GenomicRanges, IRanges, data.table, methods Suggests: knitr, pepDat License: Artistic-2.0 MD5sum: 0e38d5e45932616453d5a646f08912eb NeedsCompilation: no Package: PWMEnrich Version: 4.34.0 Depends: R (>= 3.5.0), methods, BiocGenerics, Biostrings Imports: grid, seqLogo, gdata, evd, S4Vectors Suggests: MotifDb, BSgenome, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr License: LGPL (>= 2) MD5sum: 1c95f91b66ee9a37e25eb425ec3753a5 NeedsCompilation: no Package: pwOmics Version: 1.30.0 Depends: R (>= 3.2) Imports: data.table, rBiopaxParser, igraph, STRINGdb, graphics, gplots, Biobase, BiocGenerics, AnnotationDbi, biomaRt, AnnotationHub, GenomicRanges, graph, grDevices, stats, utils Suggests: ebdbNet, longitudinal, Mfuzz License: GPL (>= 2) MD5sum: cb288b27c48b06fd430bc6f2bffbfb4d NeedsCompilation: no Package: pwrEWAS Version: 1.12.0 Depends: shinyBS, foreach Imports: doParallel, abind, truncnorm, CpGassoc, shiny, ggplot2, parallel, shinyWidgets, BiocManager, doSNOW, limma, genefilter, stats, grDevices, methods, utils, graphics, pwrEWAS.data Suggests: knitr, RUnit, BiocGenerics, rmarkdown License: Artistic-2.0 MD5sum: 1dba43c7af73d8ff0c270b3c7a4380d9 NeedsCompilation: no Package: qckitfastq Version: 1.14.0 Imports: magrittr, ggplot2, dplyr, seqTools, zlibbioc, data.table, reshape2, grDevices, graphics, stats, utils, Rcpp, rlang, RSeqAn LinkingTo: Rcpp, RSeqAn Suggests: knitr, rmarkdown, kableExtra, testthat License: Artistic-2.0 MD5sum: 8acd24f1897e667998346af3b2234562 NeedsCompilation: yes Package: qcmetrics Version: 1.36.0 Depends: R (>= 3.3) Imports: Biobase, methods, knitr, tools, xtable, pander, S4Vectors Suggests: affy, MSnbase, ggplot2, lattice, mzR, BiocStyle, rmarkdown License: GPL-2 MD5sum: f626ab88d5050d30c030ededbcac0029 NeedsCompilation: no Package: QDNAseq Version: 1.34.0 Depends: R (>= 3.1.0) Imports: graphics, methods, stats, utils, Biobase (>= 2.18.0), CGHbase (>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0), GenomicRanges (>= 1.20), IRanges (>= 2.2), matrixStats (>= 0.60.0), R.utils (>= 2.9.0), Rsamtools (>= 1.20), future.apply (>= 1.8.1) Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>= 0.6.20), GenomeInfoDb (>= 1.6.0), future (>= 1.22.1), parallelly (>= 1.28.1), R.cache (>= 0.13.0), QDNAseq.hg19, QDNAseq.mm10 License: GPL MD5sum: b4ee187a398ad47ca39997dac68121bf NeedsCompilation: no Package: QFeatures Version: 1.8.0 Depends: R (>= 4.0), MultiAssayExperiment Imports: methods, stats, utils, S4Vectors, IRanges, SummarizedExperiment, BiocGenerics, ProtGenerics (>= 1.27.1), AnnotationFilter, lazyeval, Biobase, MsCoreUtils (>= 1.7.2), igraph, plotly Suggests: SingleCellExperiment, Matrix, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, magrittr, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap License: Artistic-2.0 MD5sum: 488137c8d538bdf55926ad143b2be1c8 NeedsCompilation: no Package: qmtools Version: 1.2.0 Depends: R (>= 4.2.0), SummarizedExperiment Imports: rlang, ggplot2, patchwork, heatmaply, methods, MsCoreUtils, stats, igraph, VIM, scales, grDevices, graphics Suggests: limma, Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute, imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: c38ff3732c74bf258aaf7c8309419bd7 NeedsCompilation: no Package: qpcrNorm Version: 1.56.0 Depends: methods, Biobase, limma, affy License: LGPL (>= 2) MD5sum: cba6ab7638108ac878a217e8d313c453 NeedsCompilation: no Package: qpgraph Version: 2.32.2 Depends: R (>= 3.5) Imports: methods, parallel, Matrix (>= 1.5-0), grid, annotate, graph (>= 1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm, qtl, Rgraphviz Suggests: RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats License: GPL (>= 2) MD5sum: 4f4f38be02f23d4fd529e350a16fcb72 NeedsCompilation: yes Package: qPLEXanalyzer Version: 1.16.1 Depends: R (>= 4.0), Biobase, MSnbase Imports: assertthat, BiocGenerics, Biostrings, dplyr (>= 1.0.0), ggdendro, ggplot2, graphics, grDevices, IRanges, limma, magrittr, preprocessCore, purrr, RColorBrewer, readr, rlang, scales, stats, stringr, tibble, tidyr, tidyselect, utils Suggests: gridExtra, knitr, qPLEXdata, rmarkdown, testthat, UniProt.ws, vdiffr License: GPL-2 MD5sum: 8759c9727fe9a0c9fc645f692d057763 NeedsCompilation: no Package: qrqc Version: 1.52.0 Depends: reshape, ggplot2, Biostrings, biovizBase, brew, xtable, testthat Imports: reshape, ggplot2, Biostrings, biovizBase, graphics, methods, plyr, stats LinkingTo: Rhtslib (>= 1.15.3) License: GPL (>= 2) MD5sum: 5160a5cd4b0aab743706c0683f3cc969 NeedsCompilation: yes Package: qsea Version: 1.24.0 Depends: R (>= 3.5) Imports: Biostrings, graphics, gtools, methods, stats, utils, HMMcopy, rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges, limma, GenomeInfoDb, BiocGenerics, grDevices, zoo, BiocParallel Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager, MASS License: GPL (>= 2) MD5sum: 0a604f35df80b9ed7eb25092382a51be NeedsCompilation: yes Package: qsmooth Version: 1.14.0 Depends: R (>= 4.0) Imports: SummarizedExperiment, utils, sva, stats, methods, graphics, Hmisc Suggests: bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat License: CC BY 4.0 MD5sum: fd62456b97bd33c2f43d44b6a7859b61 NeedsCompilation: no Package: QSutils Version: 1.16.0 Depends: R (>= 3.5), Biostrings, BiocGenerics,methods Imports: ape, stats, psych Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: file LICENSE MD5sum: 209a73c83f1e1d14e3cb5a37ca8a1ff2 NeedsCompilation: no Package: qsvaR Version: 1.2.0 Depends: R (>= 4.2), SummarizedExperiment Imports: sva, stats, ggplot2, methods Suggests: BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 9602d179c2f581069f9a4b087970efa7 NeedsCompilation: no Package: Qtlizer Version: 1.12.0 Depends: R (>= 3.6.0) Imports: httr, curl, GenomicRanges, stringi Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 6d96f4069a4810bcd6075318c81f5859 NeedsCompilation: no Package: quantiseqr Version: 1.6.0 Depends: R (>= 4.1.0) Imports: Biobase, limSolve, MASS, methods, preprocessCore, stats, SummarizedExperiment, ggplot2, tidyr, rlang, utils Suggests: AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery, knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat, tibble License: GPL-3 MD5sum: a206d54e9604ca8abf52262aaf2ace76 NeedsCompilation: no Package: quantro Version: 1.32.0 Depends: R (>= 4.0) Imports: Biobase, minfi, doParallel, foreach, iterators, ggplot2, methods, RColorBrewer Suggests: rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle License: GPL (>= 3) MD5sum: 5f425a675de0aa7eb4fdee07957d45fb NeedsCompilation: no Package: quantsmooth Version: 1.64.0 Depends: R(>= 2.10.0), quantreg, grid License: GPL-2 MD5sum: a3b72d73ec34992c96358e6a40c1f23a NeedsCompilation: no Package: QuartPAC Version: 1.30.0 Depends: iPAC, GraphPAC, SpacePAC, data.table Suggests: RUnit, BiocGenerics, rgl License: GPL-2 MD5sum: 458eee6216190923282938c4f7efe2ad NeedsCompilation: no Package: QuasR Version: 1.38.0 Depends: R (>= 4.1), parallel, GenomicRanges, Rbowtie Imports: methods, grDevices, graphics, utils, stats, tools, BiocGenerics, S4Vectors, IRanges, Biobase, Biostrings, BSgenome, Rsamtools (>= 2.13.1), GenomicFeatures, ShortRead, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, AnnotationDbi LinkingTo: Rhtslib (>= 1.99.1) Suggests: Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat License: GPL-2 Archs: x64 MD5sum: cb3295e2142d0403ebed9b9dea91fb34 NeedsCompilation: yes Package: QuaternaryProd Version: 1.32.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.3), dplyr, yaml (>= 2.1.18) LinkingTo: Rcpp Suggests: knitr License: GPL (>= 3) MD5sum: d61d33fad8042df683fe0cd0ead521f4 NeedsCompilation: yes Package: QUBIC Version: 1.26.0 Depends: R (>= 3.1), biclust Imports: Rcpp (>= 0.11.0), methods, Matrix LinkingTo: Rcpp, RcppArmadillo Suggests: QUBICdata, qgraph, fields, knitr, rmarkdown Enhances: RColorBrewer License: CC BY-NC-ND 4.0 + file LICENSE MD5sum: 84ade7f60f97118609cdd8c9e5616c1b NeedsCompilation: yes Package: qusage Version: 2.32.0 Depends: R (>= 2.10), limma (>= 3.14), methods Imports: utils, Biobase, nlme, emmeans, fftw License: GPL (>= 2) MD5sum: 10d8ea7b83a72ec1698c272e9c689d7c NeedsCompilation: no Package: qvalue Version: 2.30.0 Depends: R(>= 2.10) Imports: splines, ggplot2, grid, reshape2 Suggests: knitr License: LGPL MD5sum: 8df957d24ededc50adfffe59a5cf39ed NeedsCompilation: no Package: R3CPET Version: 1.30.0 Depends: R (>= 3.2), Rcpp (>= 0.10.4), methods Imports: methods, parallel, ggplot2, pheatmap, clValid, igraph, data.table, reshape2, Hmisc, RCurl, BiocGenerics, S4Vectors, IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8), ggbio LinkingTo: Rcpp Suggests: BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny, ChIPpeakAnno License: GPL (>= 2) MD5sum: 50c53785d011680d0b7bad11e7d46bfe NeedsCompilation: yes Package: r3Cseq Version: 1.44.0 Depends: GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue Imports: methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf, RColorBrewer Suggests: BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Rnorvegicus.UCSC.rn5.masked License: GPL-3 MD5sum: 8270b483b87c8a464227fb7eecea6d29 NeedsCompilation: no Package: R453Plus1Toolbox Version: 1.48.0 Depends: R (>= 2.12.0), methods, VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6), Biobase Imports: utils, grDevices, graphics, stats, tools, xtable, R2HTML, TeachingDemos, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector, GenomicRanges (>= 1.31.8), SummarizedExperiment, biomaRt, BSgenome (>= 1.47.3), Rsamtools, ShortRead (>= 1.37.1) Suggests: rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2 License: LGPL-3 MD5sum: cebbe93dd4b6321fee66e4fd9dd68283 NeedsCompilation: yes Package: R4RNA Version: 1.26.0 Depends: R (>= 3.2.0), Biostrings (>= 2.38.0) License: GPL-3 MD5sum: c92ae6b2df10b48aa1fd0d2e55d8c0a9 NeedsCompilation: no Package: RadioGx Version: 2.2.0 Depends: R (>= 4.1), CoreGx Imports: SummarizedExperiment, BiocGenerics, data.table, S4Vectors, Biobase, parallel, BiocParallel, RColorBrewer, caTools, magicaxis, methods, reshape2, scales, grDevices, graphics, stats, utils, assertthat, matrixStats, downloader Suggests: rmarkdown, BiocStyle, knitr, pander, markdown License: GPL-3 MD5sum: 0a791da693d9633d29a2667c10bc11c3 NeedsCompilation: no Package: RaggedExperiment Version: 1.22.0 Depends: R (>= 4.2.0), GenomicRanges (>= 1.37.17) Imports: BiocGenerics, GenomeInfoDb, IRanges, Matrix, MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment License: Artistic-2.0 MD5sum: c1759ca69795e95282a7add9c41cb1ec NeedsCompilation: no Package: rain Version: 1.32.0 Depends: R (>= 2.10), gmp, multtest Suggests: lattice, BiocStyle License: GPL-2 MD5sum: 2727d6e2dcef610fb25cb16c01593b53 NeedsCompilation: no Package: rama Version: 1.72.0 Depends: R(>= 2.5.0) License: GPL (>= 2) MD5sum: f4fbe17e7330758a606a80ba412234ed NeedsCompilation: yes Package: ramr Version: 1.6.0 Depends: R (>= 4.1), GenomicRanges, parallel, doParallel, foreach, doRNG, methods Imports: IRanges, BiocGenerics, ggplot2, reshape2, EnvStats, ExtDist, matrixStats, S4Vectors Suggests: RUnit, knitr, rmarkdown, gridExtra, annotatr, LOLA, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 29f6c32a7bfd70010dd7820e4cb6359d NeedsCompilation: no Package: ramwas Version: 1.22.0 Depends: R (>= 3.3.0), methods, filematrix Imports: graphics, stats, utils, digest, glmnet, KernSmooth, grDevices, GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings, BiocGenerics Suggests: knitr, rmarkdown, pander, BiocStyle, BSgenome.Ecoli.NCBI.20080805 License: LGPL-3 MD5sum: 4b7c596c895c8537eaa99001d49b345a NeedsCompilation: yes Package: RandomWalkRestartMH Version: 1.18.0 Depends: R(>= 3.5.0) Imports: igraph, Matrix, dnet, methods Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 548d626d295812b7373b87dc79bfd4db NeedsCompilation: no Package: randPack Version: 1.44.0 Depends: methods Imports: Biobase License: Artistic-2.0 MD5sum: e6bea184510b9fd62603424a6cd36c20 NeedsCompilation: no Package: randRotation Version: 1.10.0 Imports: methods, graphics, utils, stats, Rdpack (>= 0.7) Suggests: knitr, BiocParallel, lme4, nlme, rmarkdown, BiocStyle, testthat (>= 2.1.0), limma, sva License: GPL-3 MD5sum: c5696fd75c67fdd5dbc56131ffb4bba3 NeedsCompilation: no Package: RankProd Version: 3.24.0 Depends: R (>= 3.2.1), stats, methods, Rmpfr, gmp Imports: graphics License: file LICENSE License_restricts_use: yes MD5sum: 10efc2575c19ca9cd5db3851fe203a2f NeedsCompilation: no Package: RAREsim Version: 1.2.0 Depends: R (>= 4.1.0) Imports: nloptr Suggests: markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 9043c5336cea1ec8608a7fcb3bfaf2b6 NeedsCompilation: no Package: RareVariantVis Version: 2.26.0 Depends: BiocGenerics, VariantAnnotation, googleVis, GenomicFeatures Imports: S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, SummarizedExperiment, GenomicScores Suggests: knitr License: Artistic-2.0 MD5sum: 7e2d9cb40b5cbd8a45bad829bcbcfb9f NeedsCompilation: no Package: rawrr Version: 1.6.1 Depends: R (>= 4.1) Imports: grDevices, graphics, stats, utils Suggests: BiocStyle (>= 2.5), ExperimentHub, knitr, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat License: GPL-3 MD5sum: eeb8c5036c1f60614bc5dccdd3f3998e NeedsCompilation: no Package: RbcBook1 Version: 1.66.0 Depends: R (>= 2.10), Biobase, graph, rpart License: Artistic-2.0 MD5sum: 80299eaecea3130ed5960e61f59ea155 NeedsCompilation: no Package: Rbec Version: 1.6.0 Imports: Rcpp (>= 1.0.6), dada2, ggplot2, readr, doParallel, foreach, grDevices, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: LGPL-3 MD5sum: 1532e84c27978606ff547a9b2103d763 NeedsCompilation: yes Package: RBGL Version: 1.74.0 Depends: graph, methods Imports: methods LinkingTo: BH Suggests: Rgraphviz, XML, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 3ae6e552c4fb6de1d33c276fd5a1446f NeedsCompilation: yes Package: RBioinf Version: 1.58.0 Depends: graph, methods Suggests: Rgraphviz License: Artistic-2.0 MD5sum: d7c872a979f365fcd98320bfac95bc99 NeedsCompilation: yes Package: rBiopaxParser Version: 2.38.0 Depends: R (>= 4.0), data.table Imports: XML Suggests: Rgraphviz, RCurl, graph, RUnit, BiocGenerics, RBGL, igraph License: GPL (>= 2) MD5sum: a37589851c633e70f5171a9e2e703b21 NeedsCompilation: no Package: RBM Version: 1.30.0 Depends: R (>= 3.2.0), limma, marray License: GPL (>= 2) MD5sum: 7311210610044808c7f93135b551e13e NeedsCompilation: no Package: Rbowtie Version: 1.38.0 Suggests: testthat, parallel, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | file LICENSE Archs: x64 MD5sum: 15be4b5120e924c4544608b20ba83732 NeedsCompilation: yes Package: Rbowtie2 Version: 2.4.2 Depends: R (>= 4.1.0) Imports: magrittr, Rsamtools Suggests: knitr, testthat (>= 3.0.0), rmarkdown License: GPL (>= 3) Archs: x64 MD5sum: 4a881ab9807bc6b0afadd15e931f4e11 NeedsCompilation: yes Package: rbsurv Version: 2.56.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), survival License: GPL (>= 2) MD5sum: 0e7812dcfcb1e0f6e8f5e09f3e2121f4 NeedsCompilation: no Package: Rbwa Version: 1.2.0 Depends: R (>= 4.1) Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE OS_type: unix MD5sum: 771ec285b2e0215069885fe866de9560 NeedsCompilation: yes Package: Rcade Version: 1.39.1 Depends: R (>= 3.5.0), methods, GenomicRanges, Rsamtools, baySeq Imports: utils, grDevices, stats, graphics, rgl, plotrix, S4Vectors (>= 0.23.19), IRanges, GenomeInfoDb, GenomicAlignments Suggests: limma, biomaRt, RUnit, BiocGenerics, BiocStyle License: GPL-2 MD5sum: 6a82670b5ab4f2c346baec87fa26f865 NeedsCompilation: no Package: RCAS Version: 1.24.0 Depends: R (>= 3.5.0), plotly (>= 4.5.2), DT (>= 0.2), data.table Imports: GenomicRanges, IRanges, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomeInfoDb (>= 1.12.0), Biostrings, rtracklayer, GenomicFeatures, rmarkdown (>= 0.9.5), genomation (>= 1.5.5), knitr (>= 1.12.3), BiocGenerics, S4Vectors, plotrix, pbapply, RSQLite, proxy, pheatmap, ggplot2, cowplot, ggseqlogo, utils, ranger, gprofiler2 Suggests: testthat, covr License: Artistic-2.0 MD5sum: 778d06ea591932daa0efe1f7b5fae85b NeedsCompilation: no Package: RCASPAR Version: 1.44.0 License: GPL (>= 3) MD5sum: b6bfd524f2ceb32562ec7957e6bab199 NeedsCompilation: no Package: rcellminer Version: 2.20.0 Depends: R (>= 3.2), Biobase, rcellminerData (>= 2.0.0) Imports: stringr, gplots, ggplot2, methods, stats, utils, shiny Suggests: knitr, RColorBrewer, sqldf, BiocGenerics, testthat, BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW, parallel, rmarkdown License: LGPL-3 + file LICENSE MD5sum: bc8436f200a8904438e7d6a5acc455d0 NeedsCompilation: no Package: rCGH Version: 1.28.0 Depends: R (>= 3.4),methods,stats,utils,graphics Imports: plyr,DNAcopy,lattice,ggplot2,grid,shiny (>= 0.11.1), limma,affy,mclust,TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db,GenomicFeatures,GenomeInfoDb,GenomicRanges,AnnotationDbi, parallel,IRanges,grDevices,aCGH Suggests: BiocStyle, knitr, BiocGenerics, RUnit License: Artistic-2.0 MD5sum: f028e9f8929fbb3bff388d82dccd5745 NeedsCompilation: no Package: RcisTarget Version: 1.18.2 Depends: R (>= 3.5.0) Imports: AUCell (>= 1.1.6), BiocGenerics, data.table, graphics, GenomeInfoDb, GenomicRanges, arrow (>= 2.0.0), dplyr, tibble, GSEABase, methods, R.utils, stats, SummarizedExperiment, S4Vectors, utils Suggests: Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, gplots, rtracklayer, igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat, visNetwork Enhances: doMC, doRNG, zoo License: GPL-3 MD5sum: e0f644d5525f83c3d0984ee27c46d6d7 NeedsCompilation: no Package: RCM Version: 1.14.0 Depends: R (>= 4.0), DBI Imports: RColorBrewer, alabama, edgeR, reshape2, tseries, stats, VGAM, ggplot2 (>= 2.2.1.9000), nleqslv, phyloseq, tensor, MASS, grDevices, graphics, methods Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 8bafb94a18f5de1fc8faea7363a06aeb NeedsCompilation: no Package: Rcpi Version: 1.34.0 Depends: R (>= 3.0.2) Imports: stats, utils, methods, RCurl, rjson, foreach, doParallel, Biostrings, GOSemSim, rcdk (>= 3.3.8) Suggests: knitr, rmarkdown, RUnit, BiocGenerics License: Artistic-2.0 | file LICENSE MD5sum: 9c328a53b58b69841594625def584f9f NeedsCompilation: no Package: RCSL Version: 1.6.0 Depends: R (>= 4.1) Imports: RcppAnnoy, igraph, NbClust, Rtsne, ggplot2, methods, pracma, umap, grDevices, graphics, stats Suggests: knitr, rmarkdown, mclust, RcppAnnoy License: GPL-3 MD5sum: 7005de8d320e579e13704af3af664242 NeedsCompilation: no Package: Rcwl Version: 1.14.0 Depends: R (>= 3.6), yaml, methods, S4Vectors Imports: utils, stats, BiocParallel, batchtools, DiagrammeR, shiny, R.utils, codetools, basilisk Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: fd40c03248d1040bdb2c0ef51869ecba NeedsCompilation: no Package: RcwlPipelines Version: 1.14.0 Depends: R (>= 3.6), Rcwl, BiocFileCache Imports: rappdirs, methods, utils, git2r, httr, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 78c64b2a8df420d4f71dfbf05efa3914 NeedsCompilation: no Package: RCX Version: 1.2.2 Depends: R (>= 4.2.0) Imports: jsonlite, plyr, igraph, methods Suggests: BiocStyle, testthat, knitr, rmarkdown, base64enc, graph License: MIT + file LICENSE MD5sum: 94b6fe61c0bf12932df4d53eb20ef15d NeedsCompilation: no Package: RCy3 Version: 2.18.0 Imports: httr, methods, RJSONIO, XML, utils, BiocGenerics, stats, graph, fs, uuid, uchardet, glue, RCurl, base64url, base64enc, IRkernel, IRdisplay, RColorBrewer, gplots Suggests: BiocStyle, knitr, rmarkdown, igraph, grDevices License: MIT + file LICENSE MD5sum: 1c5ce5d734cb43e0ebf1518afd03952e NeedsCompilation: no Package: RCyjs Version: 2.20.0 Depends: R (>= 3.5.0), BrowserViz (>= 2.7.18), graph (>= 1.56.0) Imports: methods, httpuv (>= 1.5.0), BiocGenerics, base64enc, utils Suggests: RUnit, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 4870cabebdb8885c99c4f4658dbe9f4e NeedsCompilation: no Package: rDGIdb Version: 1.24.0 Imports: jsonlite,httr,methods,graphics Suggests: BiocStyle,knitr,testthat License: MIT + file LICENSE MD5sum: ab8974b7e49b4eda6db71ed9502396eb NeedsCompilation: no Package: Rdisop Version: 1.58.0 Depends: R (>= 2.0.0), Rcpp LinkingTo: Rcpp Suggests: RUnit License: GPL-2 MD5sum: 1e641147bc1679a9bcb467e0344675fa NeedsCompilation: yes Package: RDRToolbox Version: 1.48.0 Depends: R (>= 2.9.0) Imports: graphics, grDevices, methods, stats, MASS, rgl Suggests: golubEsets License: GPL (>= 2) MD5sum: 06a9621b7cb5a07a65149f773fad09f3 NeedsCompilation: no Package: ReactomeContentService4R Version: 1.6.0 Imports: httr, jsonlite, utils, magick (>= 2.5.1), data.table, doParallel, foreach, parallel Suggests: pdftools, testthat, knitr, rmarkdown License: Apache License (>= 2.0) | file LICENSE MD5sum: 1bd9ccae307eac6f9d411110d9c37ccc NeedsCompilation: no Package: ReactomeGraph4R Version: 1.6.0 Depends: R (>= 4.1) Imports: neo4r, utils, getPass, jsonlite, purrr, magrittr, data.table, rlang, ReactomeContentService4R, doParallel, parallel, foreach Suggests: knitr, rmarkdown, testthat, stringr, networkD3, visNetwork, wesanderson License: Apache License (>= 2) MD5sum: 0709eab7151b9846f79000ca55834b0a NeedsCompilation: no Package: ReactomeGSA Version: 1.12.0 Imports: jsonlite, httr, progress, ggplot2, methods, gplots, RColorBrewer, dplyr, tidyr Suggests: testthat, knitr, rmarkdown, ReactomeGSA.data, Biobase, devtools Enhances: limma, edgeR, Seurat (>= 3.0), scater License: MIT + file LICENSE MD5sum: 02790814f0f95a1c8add9fb8bdecdeee NeedsCompilation: no Package: ReactomePA Version: 1.42.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, DOSE (>= 3.5.1), enrichplot, ggplot2 (>= 3.3.5), ggraph, reactome.db, igraph, graphite, gson Suggests: BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat License: GPL-2 MD5sum: b790f73ac9a2525ef354ba60162f8d16 NeedsCompilation: no Package: ReadqPCR Version: 1.44.0 Depends: R(>= 2.14.0), Biobase, methods Suggests: qpcR License: LGPL-3 MD5sum: 298d2504fffbaf4bc062eb817b19d166 NeedsCompilation: no Package: REBET Version: 1.16.0 Depends: ASSET Imports: stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: b52758b2e523c69de1785c983247e217 NeedsCompilation: yes Package: rebook Version: 1.8.0 Imports: utils, methods, knitr (>= 1.32), rmarkdown, CodeDepends, dir.expiry, filelock, BiocStyle Suggests: testthat, igraph, XML, BiocManager, RCurl, bookdown, rappdirs, yaml, BiocParallel, OSCA.intro, OSCA.workflows License: GPL-3 MD5sum: 3ded885d23e56eff97ceb55783bb2404 NeedsCompilation: no Package: receptLoss Version: 1.10.0 Depends: R (>= 3.6.0) Imports: dplyr, ggplot2, magrittr, tidyr, SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 2.1.0), here License: GPL-3 + file LICENSE MD5sum: 7709521ab2945d212720bf1e95e87680 NeedsCompilation: no Package: reconsi Version: 1.10.0 Imports: phyloseq, ks, reshape2, ggplot2, stats, methods, graphics, grDevices, matrixStats, Matrix Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 6230782936e0da12933805c5b6581ddd NeedsCompilation: no Package: recount Version: 1.24.1 Depends: R (>= 3.5.0), SummarizedExperiment Imports: BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb, GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer (>= 1.35.3), S4Vectors, stats, utils Suggests: AnnotationDbi, BiocManager, BiocStyle (>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport (>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap, DT, edgeR, ggplot2, RColorBrewer License: Artistic-2.0 MD5sum: 7b1e5f6baba505fb5f7d3d601c9a64aa NeedsCompilation: no Package: recount3 Version: 1.8.0 Depends: SummarizedExperiment Imports: BiocFileCache, methods, rtracklayer, S4Vectors, utils, RCurl, data.table, R.utils, Matrix, GenomicRanges, sessioninfo, tools Suggests: BiocStyle, covr, knitcitations, knitr, RefManageR, rmarkdown, testthat, pryr, interactiveDisplayBase, recount License: Artistic-2.0 MD5sum: 285ed605ac98b391776dd70704e8157e NeedsCompilation: no Package: recountmethylation Version: 1.8.6 Depends: R (>= 4.1) Imports: minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl, R.utils, BiocFileCache, basilisk, reticulate, DelayedMatrixStats Suggests: minfiData, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub License: Artistic-2.0 MD5sum: de137c76f378f5b187e5fca8f4bb1161 NeedsCompilation: no Package: recoup Version: 1.26.0 Depends: R (>= 4.0.0), GenomicRanges, GenomicAlignments, ggplot2, ComplexHeatmap Imports: BiocGenerics, biomaRt, Biostrings, circlize, GenomeInfoDb, GenomicFeatures, graphics, grDevices, httr, IRanges, methods, parallel, RSQLite, Rsamtools, rtracklayer, S4Vectors, stats, stringr, utils Suggests: grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RMySQL License: GPL (>= 3) MD5sum: 820478d6a78305a13e8c729a2469242e NeedsCompilation: no Package: RedeR Version: 2.2.1 Depends: R (>= 4.0), methods Imports: igraph Suggests: BiocStyle, knitr, rmarkdown, markdown, TreeAndLeaf License: GPL (>= 3) MD5sum: 42e85cbfccbc537a1b7a793e9628eed1 NeedsCompilation: no Package: RedisParam Version: 1.0.0 Depends: R (>= 4.2.0), BiocParallel (>= 1.29.12) Imports: methods, redux, withr, futile.logger Suggests: rmarkdown, knitr, testthat, BiocStyle License: Artistic-2.0 MD5sum: 9858ca0a5ecb9faabe3b9decf2df6987 NeedsCompilation: no Package: REDseq Version: 1.44.0 Depends: R (>= 3.5.0), BiocGenerics, BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno Imports: AnnotationDbi, graphics, IRanges (>= 1.13.5), stats, utils License: GPL (>= 2) MD5sum: 4383a3e9c1f57e376cdeddcd377c547a NeedsCompilation: no Package: RefPlus Version: 1.68.0 Depends: R (>= 2.8.0), Biobase (>= 2.1.0), affy (>= 1.20.0), affyPLM (>= 1.18.0), preprocessCore (>= 1.4.0) Suggests: affydata License: GPL (>= 2) MD5sum: 654073024eab6c9d742588c40d00bdf2 NeedsCompilation: no Package: RegEnrich Version: 1.8.0 Depends: R (>= 4.0.0), S4Vectors, dplyr, tibble, BiocSet, SummarizedExperiment Imports: randomForest, fgsea, DOSE, BiocParallel, DESeq2, limma, WGCNA, ggplot2 (>= 2.2.0), methods, reshape2, magrittr Suggests: GEOquery, rmarkdown, knitr, BiocManager, testthat License: GPL (>= 2) MD5sum: d6b858adec1e59b2cf1c01e83ffafe25 NeedsCompilation: no Package: regioneR Version: 1.30.0 Depends: GenomicRanges Imports: memoise, GenomicRanges, IRanges, BSgenome, Biostrings, rtracklayer, parallel, graphics, stats, utils, methods, GenomeInfoDb, S4Vectors, tools Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19.masked, testthat License: Artistic-2.0 MD5sum: 058b9446d7ccc48a690df062dc59c6cc NeedsCompilation: no Package: regioneReloaded Version: 1.0.0 Depends: R (>= 4.2), regioneR Imports: stats, RColorBrewer, Rtsne, umap, ggplot2, ggrepel, reshape2, methods, scales, cluster, grid, grDevices Suggests: rmarkdown, BiocStyle, GenomeInfoDb, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 0ab6f8fe7ab85f591e22d2642e8fdf9c NeedsCompilation: no Package: regionReport Version: 1.32.0 Depends: R(>= 3.2) Imports: BiocStyle (>= 2.5.19), derfinder (>= 1.25.3), DEFormats, DESeq2, GenomeInfoDb, GenomicRanges, knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR, rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment, utils Suggests: BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot (>= 1.29.1), sessioninfo, DT, edgeR, ggbio (>= 1.35.2), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker License: Artistic-2.0 MD5sum: b6092e9d7af84477fd0bb5ab73197eb8 NeedsCompilation: no Package: regsplice Version: 1.24.0 Imports: glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats, pbapply, utils, methods Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 546b47268a1484299a1444b01178af01 NeedsCompilation: no Package: regutools Version: 1.10.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, Biostrings, DBI, GenomicRanges, Gviz, IRanges, RCy3, RSQLite, S4Vectors, methods, stats, utils, BiocFileCache Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr License: Artistic-2.0 MD5sum: 7a5a4dea46c3d14a8fae25f77fc8a3e1 NeedsCompilation: no Package: REMP Version: 1.22.0 Depends: R (>= 3.6), SummarizedExperiment(>= 1.1.6), minfi (>= 1.22.0) Imports: readr, rtracklayer, graphics, stats, utils, methods, settings, BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel, doParallel, parallel, foreach, caret, kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db, impute, iterators Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC License: GPL-3 MD5sum: c933c7b3feb7f5aa6daed4b1e71bb10c NeedsCompilation: no Package: Repitools Version: 1.44.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.8.0) Imports: parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, BSgenome (>= 1.47.3), gplots, grid, MASS, gsmoothr, edgeR (>= 3.4.0), DNAcopy, Ringo, Rsolnp, cluster Suggests: ShortRead, BSgenome.Hsapiens.UCSC.hg18 License: LGPL (>= 2) MD5sum: a39f510b1663ce55c1efaeddb3f4b98b NeedsCompilation: yes Package: ReportingTools Version: 2.38.0 Depends: methods, knitr, utils Imports: Biobase,hwriter,Category,GOstats,limma(>= 3.17.5),lattice,AnnotationDbi,edgeR, annotate,PFAM.db, GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils, DESeq2(>= 1.3.41), ggplot2, ggbio, IRanges Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db, rmarkdown, markdown License: Artistic-2.0 MD5sum: 84577f6262b4ac78035b6363fe918e36 NeedsCompilation: no Package: RepViz Version: 1.14.0 Depends: R (>= 3.5.1), GenomicRanges (>= 1.30.0), Rsamtools (>= 1.34.1), IRanges (>= 2.14.0), biomaRt (>= 2.36.0), S4Vectors (>= 0.18.0), graphics, grDevices, utils Suggests: rmarkdown, knitr, testthat License: GPL-3 MD5sum: 1b3d39fe1ea906228a5f586d40ce8950 NeedsCompilation: no Package: ReQON Version: 1.44.0 Depends: R (>= 3.0.2), Rsamtools, seqbias Imports: rJava, graphics, stats, utils, grDevices Suggests: BiocStyle License: GPL-2 MD5sum: 40f412c9035e8a24cfbb944a5fd55fe2 NeedsCompilation: no Package: ResidualMatrix Version: 1.8.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular License: GPL-3 MD5sum: 68e68610b5928669376b8e3b17f2bfc8 NeedsCompilation: no Package: RESOLVE Version: 1.0.0 Depends: R (>= 3.5.0), NMF Imports: Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5, cluster, data.table, GenomeInfoDb, GenomicRanges, glmnet, ggplot2, gridExtra, IRanges, lsa, nnls, parallel, reshape2 Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: c3143f8a49a31bab8b10b594921fc2cd NeedsCompilation: no Package: restfulSE Version: 1.20.0 Depends: R (>= 3.6), SummarizedExperiment,DelayedArray Imports: utils, stats, methods, S4Vectors, Biobase,reshape2, AnnotationDbi, DBI, GO.db, rhdf5client, dplyr (>= 0.7.1), magrittr, bigrquery, ExperimentHub, AnnotationHub, rlang Suggests: knitr, testthat, Rtsne, org.Mm.eg.db, org.Hs.eg.db, BiocStyle, restfulSEData, rmarkdown License: Artistic-2.0 MD5sum: f8668cef27e54b75af55768530c119ba NeedsCompilation: no Package: rexposome Version: 1.20.1 Depends: R (>= 3.5), Biobase Imports: methods, utils, stats, lsr, FactoMineR, stringr, circlize, corrplot, ggplot2, reshape2, pryr, S4Vectors, imputeLCMD, scatterplot3d, glmnet, gridExtra, grid, Hmisc, gplots, gtools, scales, lme4, grDevices, graphics, ggrepel, mice Suggests: mclust, flexmix, testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: f0885765411130c947d08ff7f300c993 NeedsCompilation: no Package: rfaRm Version: 1.10.2 Imports: httr, stringi, rsvg, magick, data.table, Biostrings, utils, rvest, xml2, IRanges, S4Vectors Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics License: GPL-3 MD5sum: 99d651dd83546eefddc2d199e6b8653b NeedsCompilation: no Package: Rfastp Version: 1.8.0 Imports: Rcpp, rjson, ggplot2, reshape2 LinkingTo: Rcpp, Rhtslib, zlibbioc Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 635fd2494d9427bb7d15e3d24eb46c2e NeedsCompilation: yes Package: rfPred Version: 1.36.0 Depends: R (>= 3.5.0), methods Imports: utils, GenomeInfoDb, data.table, IRanges, GenomicRanges, parallel, Rsamtools Suggests: BiocStyle License: GPL (>= 2) MD5sum: f7bfb56b1482c97ea84264c7d225b9da NeedsCompilation: yes Package: rGADEM Version: 2.46.0 Depends: R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo Imports: Biostrings, GenomicRanges, methods, graphics, seqLogo Suggests: BSgenome.Hsapiens.UCSC.hg19, rtracklayer License: Artistic-2.0 MD5sum: 3bd011a34a31b945502400d3f88663f0 NeedsCompilation: yes Package: rGenomeTracks Version: 1.4.0 Depends: R (>= 4.1.0), Imports: imager, reticulate, methods, rGenomeTracksData Suggests: rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: cef5b377820ebf33e618194cc43d0a10 NeedsCompilation: no Package: RGMQL Version: 1.18.0 Depends: R(>= 3.4.2), RGMQLlib Imports: httr, rJava, GenomicRanges, rtracklayer, data.table, utils, plyr, xml2, methods, S4Vectors, dplyr, stats, glue, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 5753849d023a2bc0672ae2a338e720a3 NeedsCompilation: no Package: RgnTX Version: 1.0.0 Depends: R (>= 4.2.0) Imports: GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, graphics, IRanges, methods, regioneR, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 66e23f6176f741f9df34c82c34749803 NeedsCompilation: no Package: rgoslin Version: 1.2.0 Imports: Rcpp (>= 1.0.3), dplyr LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra, BiocManager, stringr, ggplot2, tibble, lipidr License: MIT + file LICENSE MD5sum: 4711132a8acf576f30e8a5b757b28a16 NeedsCompilation: yes Package: RGraph2js Version: 1.26.0 Imports: utils, whisker, rjson, digest, graph Suggests: RUnit, BiocStyle, BiocGenerics, xtable, sna License: GPL-2 MD5sum: 8a2ad6a9c701b812bec6ff8c6307db18 NeedsCompilation: no Package: Rgraphviz Version: 2.42.0 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: stats4, graphics, grDevices Suggests: RUnit, BiocGenerics, XML License: EPL MD5sum: 53f3f39cce41cc63cf99893bff0b0e10 NeedsCompilation: yes Package: rGREAT Version: 2.0.2 Depends: R (>= 3.6.0), GenomicRanges, IRanges, methods Imports: graphics, rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats, GlobalOptions, shiny, DT, GenomicFeatures, digest, GO.db, progress, circlize, AnnotationDbi, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, RColorBrewer, S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db Enhances: BioMartGOGeneSets, UniProtKeywords License: MIT + file LICENSE MD5sum: dc311aa9d4fe0ace42cd1b745b57f2b1 NeedsCompilation: yes Package: RGSEA Version: 1.32.0 Depends: R(>= 2.10.0) Imports: BiocGenerics Suggests: BiocStyle, GEOquery, knitr, RUnit License: GPL (>= 3) MD5sum: 793958b5ea6408a64a55838f698cb546 NeedsCompilation: no Package: rgsepd Version: 1.30.0 Depends: R (>= 4.2.0), DESeq2, goseq (>= 1.28) Imports: gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, AnnotationDbi Suggests: boot, tools, BiocGenerics, knitr, xtable License: GPL-3 MD5sum: 1957660c4375ac94ed69d359c1e6ec3e NeedsCompilation: no Package: rhdf5 Version: 2.42.1 Depends: R (>= 4.0.0), methods Imports: Rhdf5lib (>= 1.13.4), rhdf5filters LinkingTo: Rhdf5lib Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, microbenchmark, dplyr, ggplot2, mockery License: Artistic-2.0 MD5sum: 3f1738ccdee045f205c6309d40ad2754 NeedsCompilation: yes Package: rhdf5client Version: 1.20.0 Depends: R (>= 3.6), methods, DelayedArray Imports: S4Vectors, httr, R6, rjson, utils Suggests: knitr, testthat, BiocStyle, DT, rmarkdown License: Artistic-2.0 MD5sum: 976fb4075570891731b3343caa40341f NeedsCompilation: yes Package: rhdf5filters Version: 1.10.1 LinkingTo: Rhdf5lib Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), rhdf5 (>= 2.34.0) License: BSD_2_clause + file LICENSE MD5sum: c9ef1a9376a1a18798c7d21415ae44b5 NeedsCompilation: yes Package: Rhdf5lib Version: 1.20.0 Depends: R (>= 4.0.0) Suggests: BiocStyle, knitr, rmarkdown, tinytest, mockery License: Artistic-2.0 MD5sum: 94c1bdfe7799bf8db8402e8a42746129 NeedsCompilation: yes Package: Rhisat2 Version: 1.14.0 Depends: R (>= 4.2) Imports: GenomicFeatures, SGSeq, GenomicRanges, methods, utils Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 Archs: x64 MD5sum: be7b01b092f63b6edc3f7489faf7724d NeedsCompilation: yes Package: Rhtslib Version: 2.0.0 Imports: zlibbioc LinkingTo: zlibbioc Suggests: knitr, rmarkdown, BiocStyle License: LGPL (>= 2) MD5sum: 69bbda8208069ab4542f23cd6249bac8 NeedsCompilation: yes Package: RiboCrypt Version: 1.4.0 Depends: R (>= 3.6.0), ORFik (>= 1.13.12) Imports: BiocGenerics, BiocParallel, Biostrings, data.table, dplyr, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, IRanges, plotly, rlang Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 0d3d1f4e4f485395cf02e0774042f1ed NeedsCompilation: no Package: RiboDiPA Version: 1.6.0 Depends: R (>= 4.1), Rsamtools, GenomicFeatures, GenomicAlignments Imports: Rcpp (>= 1.0.2), graphics, stats, data.table, elitism, methods, S4Vectors, IRanges, GenomicRanges, matrixStats, reldist, doParallel, foreach, parallel, qvalue, DESeq2, ggplot2, BiocFileCache,BiocGenerics LinkingTo: Rcpp Suggests: knitr, rmarkdown License: LGPL (>= 3) MD5sum: e8256bc14cbb0443dcd9ded275652dae NeedsCompilation: yes Package: RiboProfiling Version: 1.28.0 Depends: R (>= 3.5.0), Biostrings Imports: BiocGenerics, GenomeInfoDb, GenomicRanges, IRanges, reshape2, GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments, ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment License: GPL-3 MD5sum: 69ebcf07adea387df2f6da033c6767cd NeedsCompilation: no Package: ribor Version: 1.10.0 Depends: R (>= 3.6.0) Imports: dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors, tidyr, tools, yaml Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 1d15ba1fb642daf684ac0402b4a7a041 NeedsCompilation: no Package: riboSeqR Version: 1.32.0 Depends: R (>= 3.0.2), methods, GenomicRanges, abind Imports: Rsamtools, IRanges, baySeq, GenomeInfoDb, seqLogo Suggests: BiocStyle, RUnit, BiocGenerics License: GPL-3 MD5sum: 07d6999d956a9cdb78814ed0458593c4 NeedsCompilation: no Package: ribosomeProfilingQC Version: 1.10.0 Depends: R (>= 4.0), GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq, GenomicAlignments, GenomicFeatures, GenomeInfoDb, IRanges, methods, motifStack, rtracklayer, Rsamtools, RUVSeq, Rsubread, S4Vectors, XVector, ggplot2, ggfittext, scales, ggrepel, utils, cluster, stats, graphics, grid Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, limma, testthat, rmarkdown License: GPL (>= 3) + file LICENSE MD5sum: b75d67094e8de9b6d1ce0fbf2482a7f7 NeedsCompilation: no Package: rifi Version: 1.2.2 Depends: R (>= 4.2) Imports: car, cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, graphics, grDevices, grid, methods, nls2, nnet, rlang, S4Vectors, scales, stats, stringr, SummarizedExperiment, tibble, rtracklayer, reshape2, utils Suggests: DescTools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: c592a86b788be8c0b3e2dccaf59e91a2 NeedsCompilation: no Package: RImmPort Version: 1.26.0 Imports: plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools, utils, RSQLite Suggests: knitr License: GPL-3 MD5sum: d0f17c5ab1c9ea60aa96050ac97a43e1 NeedsCompilation: no Package: Ringo Version: 1.62.0 Depends: methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix, grid, lattice Imports: BiocGenerics (>= 0.1.11), genefilter, limma, vsn, stats4 Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0) License: Artistic-2.0 MD5sum: 2e4a7a0c02ca130b32ff6913bd26b98f NeedsCompilation: yes Package: RIPAT Version: 1.8.0 Depends: R (>= 4.0) Imports: biomaRt (>= 2.38.0), GenomicRanges (>= 1.34.0), ggplot2 (>= 3.1.0), grDevices (>= 3.5.3), IRanges (>= 2.16.0), karyoploteR (>= 1.6.3), openxlsx (>= 4.1.4), plyr (>= 1.8.4), regioneR (>= 1.12.0), rtracklayer (>= 1.42.2), stats (>= 3.5.3), stringr (>= 1.3.1), utils (>= 3.5.3) Suggests: knitr (>= 1.28) License: Artistic-2.0 MD5sum: af75f0db8c39ffdd47c4bc2ff540dfdd NeedsCompilation: no Package: Risa Version: 1.40.0 Depends: R (>= 2.0.9), Biobase (>= 2.4.0), methods, Rcpp (>= 0.9.13), biocViews, affy Imports: xcms Suggests: faahKO (>= 1.2.11) License: LGPL MD5sum: f3a143d3d3d6227b470cb7250ad85b1d NeedsCompilation: no Package: RITAN Version: 1.22.0 Depends: R (>= 4.0), Imports: graphics, methods, stats, utils, grid, gridExtra, reshape2, gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL, linkcomm, dynamicTreeCut, gsubfn, hash, png, sqldf, igraph, BgeeDB, knitr, RITANdata, GenomicFeatures, ensembldb, AnnotationFilter, EnsDb.Hsapiens.v86 Suggests: rmarkdown, BgeeDB License: file LICENSE MD5sum: a8dcfeeb948815e71512c416e2ffde4d NeedsCompilation: no Package: RIVER Version: 1.22.0 Depends: R (>= 3.3.2) Imports: glmnet, pROC, ggplot2, graphics, stats, Biobase, methods, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools License: GPL (>= 2) MD5sum: d7592fc63617d3953faf25ee6e914898 NeedsCompilation: no Package: RJMCMCNucleosomes Version: 1.22.0 Depends: R (>= 3.5.0), IRanges, GenomicRanges Imports: Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb, S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit License: Artistic-2.0 MD5sum: 13f0bef565919e760daeb34ac8c1ed77 NeedsCompilation: yes Package: RLassoCox Version: 1.6.0 Depends: R (>= 4.1), glmnet Imports: Matrix, igraph, survival, stats Suggests: knitr License: Artistic-2.0 MD5sum: fdad9f6cddc138b8e40affbb5d1ab282 NeedsCompilation: no Package: RLMM Version: 1.60.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) MD5sum: ba8d5ca06b8a03930c3adad02cb17d46 NeedsCompilation: no Package: RLSeq Version: 1.4.1 Depends: R (>= 4.2.0) Imports: dplyr, ggplot2, RColorBrewer, grid, regioneR, valr, caretEnsemble, GenomicFeatures, rtracklayer, GenomicRanges, GenomeInfoDb, ComplexHeatmap, AnnotationHub, VennDiagram, callr, circlize, ggplotify, ggprism, methods, stats, RLHub, aws.s3, pheatmap Suggests: AnnotationDbi, BiocStyle, covr, lintr, rcmdcheck, DT, httr, jsonlite, kableExtra, kernlab, knitr, magick, MASS, org.Hs.eg.db, R.utils, randomForest, readr, rmarkdown, rpart, testthat (>= 3.0.0), tibble, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, futile.logger License: MIT + file LICENSE MD5sum: 574465cbee2a9a0f273cf22cf2144415 NeedsCompilation: no Package: Rmagpie Version: 1.54.0 Depends: R (>= 2.6.1), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab, methods, pamr, stats, utils Suggests: xtable License: GPL (>= 3) MD5sum: 2e46ad876812d2e0b10e5dd387948efb NeedsCompilation: no Package: RMassBank Version: 3.8.0 Depends: Rcpp Imports: XML,rjson,S4Vectors,digest, rcdk,yaml,mzR,methods,Biobase,MSnbase,httr, enviPat,assertthat,logger,RCurl,readJDX,webchem, ChemmineR,ChemmineOB,R.utils,data.table Suggests: BiocStyle,gplots,RMassBankData (>= 1.33.1), xcms (>= 1.37.1), CAMERA, RUnit, knitr, rmarkdown License: Artistic-2.0 MD5sum: fb5e0c2bc7113a7cf707e01cb72bf83a NeedsCompilation: no Package: rmelting Version: 1.14.0 Depends: R (>= 3.6) Imports: Rdpack, rJava (>= 0.9-8) Suggests: readxl, knitr, rmarkdown, reshape2, pander, testthat License: GPL-2 | GPL-3 MD5sum: 61776c6d6e654ff8a8a430ea4e376135 NeedsCompilation: no Package: Rmmquant Version: 1.16.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.12.8), methods, S4Vectors, GenomicRanges, SummarizedExperiment, devtools, TBX20BamSubset, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, DESeq2, BiocStyle LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 10a7f4e42f1fbfa2653ab72f748a4a97 NeedsCompilation: yes Package: rmspc Version: 1.4.0 Imports: processx, BiocManager, rtracklayer, stats, tools, methods, GenomicRanges, stringr Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 2ceb1a7afc515c44eda59089a935f064 NeedsCompilation: no Package: RNAAgeCalc Version: 1.10.0 Depends: R (>= 3.6) Imports: ggplot2, recount, impute, AnnotationDbi, org.Hs.eg.db, stats, SummarizedExperiment, methods Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 36c3488fd5f1e60e51396f846f3e9ee9 NeedsCompilation: no Package: RNAdecay Version: 1.18.0 Depends: R (>= 3.5) Imports: stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr, scales Suggests: parallel, knitr, reshape2, rmarkdown License: GPL-2 MD5sum: 6fc34db27bfa3adbeddc37f13b385431 NeedsCompilation: yes Package: rnaEditr Version: 1.8.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, BiocGenerics, GenomeInfoDb, bumphunter, S4Vectors, stats, survival, logistf, plyr, corrplot Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: d1236593240da671fec255aebcebc538 NeedsCompilation: no Package: RNAinteract Version: 1.46.0 Depends: R (>= 2.12.0), Imports: RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid, hwriter, lattice, latticeExtra, limma, methods, splots (>= 1.13.12), abind, locfit, Biobase License: Artistic-2.0 MD5sum: 8bb5a4719e28588198ef2d949444e15c NeedsCompilation: no Package: RNAmodR Version: 1.12.0 Depends: R (>= 4.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomicRanges, Modstrings Imports: methods, stats, grDevices, matrixStats, BiocGenerics, Biostrings (>= 2.57.2), BiocParallel, GenomicFeatures, GenomicAlignments, GenomeInfoDb, rtracklayer, Rsamtools, BSgenome, RColorBrewer, colorRamps, ggplot2, Gviz (>= 1.31.0), reshape2, graphics, ROCR Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data License: Artistic-2.0 MD5sum: ffc590bdc29767d0f7e5b5214c4d51a6 NeedsCompilation: no Package: RNAmodR.AlkAnilineSeq Version: 1.12.0 Depends: R (>= 4.0), RNAmodR (>= 1.5.3) Imports: methods, S4Vectors, IRanges, BiocGenerics, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, Biostrings, RNAmodR.Data License: Artistic-2.0 MD5sum: c34aa61fbe750cf796b0efe49f7c4c96 NeedsCompilation: no Package: RNAmodR.ML Version: 1.12.0 Depends: R (>= 3.6), RNAmodR Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, stats, ranger Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data, RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer, keras License: Artistic-2.0 MD5sum: 328af6dc93c4fc57c1a9634bffc9644d NeedsCompilation: no Package: RNAmodR.RiboMethSeq Version: 1.12.0 Depends: R (>= 4.0), RNAmodR (>= 1.5.3) Imports: methods, S4Vectors, BiocGenerics, IRanges, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, RNAmodR.Data License: Artistic-2.0 MD5sum: 9330b608c5821c0e5adc5aa6f6ead134 NeedsCompilation: no Package: RNAsense Version: 1.12.0 Depends: R (>= 3.6) Imports: ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment, stats, utils, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: f39a13936ffc9fd834f13ef73501ccc6 NeedsCompilation: no Package: rnaseqcomp Version: 1.28.0 Depends: R (>= 3.2.0) Imports: RColorBrewer, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 611658a8e336b5d26aff7894cb6139a1 NeedsCompilation: no Package: RNASeqPower Version: 1.38.0 License: LGPL (>= 2) MD5sum: fbfe16cd2fa94de1cf5e8697dc4b6641 NeedsCompilation: no Package: RNASeqR Version: 1.16.0 Depends: R(>= 3.5.0), ggplot2, pathview, edgeR, methods Imports: Rsamtools, tools, reticulate, ballgown, gridExtra, rafalib, FactoMineR, factoextra, corrplot, PerformanceAnalytics, reshape2, DESeq2, systemPipeR, systemPipeRdata, clusterProfiler, org.Hs.eg.db, org.Sc.sgd.db, stringr, pheatmap, grDevices, graphics, stats, utils, DOSE, Biostrings, parallel Suggests: knitr, rmarkdown, png, grid, RNASeqRData License: Artistic-2.0 MD5sum: 957128c7b72e128e679f361bb3a752ac NeedsCompilation: no Package: RnaSeqSampleSize Version: 2.8.0 Depends: R (>= 4.0.0), ggplot2, RnaSeqSampleSizeData Imports: biomaRt,edgeR,heatmap3,matlab,KEGGREST,methods,grDevices, graphics, stats, Rcpp (>= 0.11.2),recount,ggpubr,SummarizedExperiment,tidyr,dplyr,tidyselect,utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 258116bb27bdb8883257301a8be3a720 NeedsCompilation: yes Package: RnBeads Version: 2.16.0 Depends: R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25), GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, grid, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr Imports: IRanges Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, GLAD, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame License: GPL-3 MD5sum: a589182da5a77954c6846027f88ae829 NeedsCompilation: no Package: roar Version: 1.34.0 Depends: R (>= 3.0.1) Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, GenomicAlignments (>= 0.99.4), rtracklayer, GenomeInfoDb Suggests: RNAseqData.HNRNPC.bam.chr14, testthat License: GPL-3 MD5sum: ec309b2755416acedf1b81eb850ab866 NeedsCompilation: no Package: ROC Version: 1.74.0 Depends: R (>= 1.9.0), utils, methods Imports: knitr Suggests: rmarkdown, Biobase License: Artistic-2.0 MD5sum: 37c04dc7d0ac3571ff0da51098afb706 NeedsCompilation: yes Package: ROCpAI Version: 1.10.0 Depends: boot, SummarizedExperiment, fission, knitr, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 351a488f137ff202e00c2bdba9838d54 NeedsCompilation: no Package: RolDE Version: 1.2.0 Depends: R (>= 4.2.0) Imports: stats, methods, ROTS, matrixStats, foreach, parallel, doParallel, doRNG, rngtools, SummarizedExperiment, nlme, qvalue, grDevices, graphics, utils Suggests: knitr, printr, rmarkdown, testthat License: GPL-3 MD5sum: 6def7800fe092da81bf592423207c43e NeedsCompilation: no Package: rols Version: 2.26.0 Depends: methods Imports: httr, progress, jsonlite, utils, Biobase, BiocGenerics (>= 0.23.1) Suggests: GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat, lubridate, DT, rmarkdown, License: GPL-2 MD5sum: 89852d10678aa99632afb99b46fffefd NeedsCompilation: no Package: ROntoTools Version: 2.26.0 Depends: methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz Suggests: RUnit, BiocGenerics License: CC BY-NC-ND 4.0 + file LICENSE MD5sum: 9de3f2e7ac9c008025e214bd844038d3 NeedsCompilation: no Package: ropls Version: 1.30.0 Depends: R (>= 3.5.0) Imports: Biobase, ggplot2, graphics, grDevices, methods, plotly, stats, MultiAssayExperiment, MultiDataSet, SummarizedExperiment, utils Suggests: BiocGenerics, BiocStyle, knitr, multtest, omicade4, rmarkdown, testthat License: CeCILL MD5sum: 99baf6dc9b10be1df94ebe46e2acde21 NeedsCompilation: no Package: ROSeq Version: 1.10.0 Depends: R (>= 4.0) Imports: pbmcapply, edgeR, limma Suggests: knitr, rmarkdown, testthat, RUnit, BiocGenerics License: GPL-3 MD5sum: fd91e8d895782c853968336bf6374d44 NeedsCompilation: no Package: ROTS Version: 1.26.0 Depends: R (>= 3.3) Imports: Rcpp, stats, Biobase, methods LinkingTo: Rcpp Suggests: testthat License: GPL (>= 2) MD5sum: 7ef71e23c0d919a79729224717aa1617 NeedsCompilation: yes Package: RPA Version: 1.54.0 Depends: R (>= 3.1.1), affy, BiocGenerics, BiocStyle, methods, rmarkdown Imports: phyloseq Suggests: affydata, knitr, parallel License: BSD_2_clause + file LICENSE MD5sum: 5e144f840d9841d93187a7ec787cf2f9 NeedsCompilation: no Package: rprimer Version: 1.2.0 Depends: R (>= 4.1) Imports: Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods, patchwork, reshape2, S4Vectors, shiny, shinycssloaders, shinyFeedback Suggests: BiocStyle, covr, kableExtra, knitr, rmarkdown, styler, testthat (>= 3.0.0) License: GPL-3 MD5sum: d52e6257578aaac63532f55e367d4696 NeedsCompilation: no Package: RProtoBufLib Version: 2.10.0 Suggests: knitr, rmarkdown License: BSD_3_clause MD5sum: 260cc9ba12583b3113df8ee9b5b06958 NeedsCompilation: yes Package: rpx Version: 2.6.3 Depends: methods Imports: BiocFileCache, jsonlite, xml2, RCurl, curl, utils Suggests: Biostrings, BiocStyle, testthat, knitr, rmarkdown License: GPL-2 MD5sum: 09b83697e4bdeed8a629368fbadd6819 NeedsCompilation: no Package: Rqc Version: 1.32.0 Depends: BiocParallel, ShortRead, ggplot2 Imports: BiocGenerics (>= 0.25.1), Biostrings, IRanges, methods, S4Vectors, knitr (>= 1.7), BiocStyle, plyr, markdown, grid, reshape2, Rcpp (>= 0.11.6), biovizBase, shiny, Rsamtools, GenomicAlignments, GenomicFiles LinkingTo: Rcpp Suggests: rmarkdown, testthat License: GPL (>= 2) MD5sum: 4986a8d601200417d208aaba1b398eb7 NeedsCompilation: yes Package: rqt Version: 1.24.0 Depends: R (>= 3.4), SummarizedExperiment Imports: stats,Matrix,ropls,methods,car,RUnit,metap,CompQuadForm,glmnet,utils,pls Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: 6218b8c085842047b75de769eae67b14 NeedsCompilation: no Package: rqubic Version: 1.44.0 Imports: methods, Biobase, BiocGenerics, biclust Suggests: RColorBrewer License: GPL-2 MD5sum: 6aef29ecd4392a4fb4fa992ce9873c35 NeedsCompilation: yes Package: rRDP Version: 1.32.0 Depends: Biostrings (>= 2.26.2) Suggests: rRDPData License: GPL-2 | file LICENSE MD5sum: 1ecfab12fa08878c4717417a6faa8a92 NeedsCompilation: no Package: RRHO Version: 1.38.0 Depends: R (>= 2.10), grid Imports: VennDiagram Suggests: lattice License: GPL-2 MD5sum: 8242c4e6e0a3584a5c89df78198d42a5 NeedsCompilation: no Package: rrvgo Version: 1.10.0 Imports: GOSemSim, AnnotationDbi, GO.db, pheatmap, ggplot2, ggrepel, treemap, tm, wordcloud, shiny, grDevices, grid, stats, methods, umap Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), shinydashboard, DT, plotly, heatmaply, magrittr, utils, clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db License: GPL-3 MD5sum: 05c1018dae1e3a96cfb76a7d87c1a281 NeedsCompilation: no Package: Rsamtools Version: 2.14.0 Depends: methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Biostrings (>= 2.47.6), R (>= 3.5.0) Imports: utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops, BiocParallel, stats LinkingTo: Rhtslib (>= 1.99.3), S4Vectors, IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle License: Artistic-2.0 | file LICENSE MD5sum: 36dc928eb8aebb85ad4f2d0098c1daf6 NeedsCompilation: yes Package: rsbml Version: 2.56.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils Imports: BiocGenerics, graph, utils License: Artistic-2.0 MD5sum: d79970f3e2ff24a8b86ade8814a3547b NeedsCompilation: yes Package: rScudo Version: 1.14.0 Depends: R (>= 3.6) Imports: methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, SummarizedExperiment, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel License: GPL-3 MD5sum: e64a20fc14cfdd102698fd0c29152efc NeedsCompilation: no Package: rsemmed Version: 1.8.0 Depends: R (>= 4.0), igraph Imports: methods, magrittr, stringr, dplyr Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: b673de6bbcfac1b1d4fbf7b02f1d1967 NeedsCompilation: no Package: RSeqAn Version: 1.18.0 Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 83ebe7d9e05c064e3e89d03b6bcdeb87 NeedsCompilation: yes Package: Rsubread Version: 2.12.3 Imports: grDevices, stats, utils, Matrix License: GPL (>= 3) MD5sum: 28dc31adea9d1f1d20f749d0a794fe9a NeedsCompilation: yes Package: RSVSim Version: 1.38.0 Depends: R (>= 3.5.0), Biostrings, GenomicRanges Imports: methods, IRanges, ShortRead Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer License: LGPL-3 MD5sum: 32fdb23588f4acb8b31801a11eeb64fb NeedsCompilation: no Package: rSWeeP Version: 1.10.0 Depends: R (>= 4.0) Imports: pracma, stats Suggests: Biostrings, methods, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 98fc57049c6c2bc16b69e85e51edb408 NeedsCompilation: no Package: RTCA Version: 1.50.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 MD5sum: 51dab9fdb0edf9e8ca093fe383231cd9 NeedsCompilation: no Package: RTCGA Version: 1.28.0 Depends: R (>= 3.3.0) Imports: XML, RCurl, assertthat, stringi, rvest, data.table, xml2, dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr, scales, rmarkdown, htmltools Suggests: devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, magrittr, tidyr License: GPL-2 MD5sum: 9982fa3d1f97e661060f8d10a05ec943 NeedsCompilation: no Package: RTCGAToolbox Version: 2.28.4 Depends: R (>= 3.5.0) Imports: BiocGenerics, data.table, DelayedArray, GenomicRanges, GenomeInfoDb, grDevices, httr, limma, methods, RaggedExperiment, RCircos, RCurl, RJSONIO, rvest, S4Vectors (>= 0.23.10), stats, stringr, SummarizedExperiment, survival, TCGAutils (>= 1.9.4), utils, XML Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown License: GPL-2 MD5sum: 05395e523033c09ea86c6b375d56e228 NeedsCompilation: no Package: RTN Version: 2.22.1 Depends: R (>= 3.6.3), methods, Imports: RedeR, minet, viper, mixtools, snow, stats, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr, pheatmap, grDevices, graphics, utils Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 1c964d15d6ab6de410e135b4565b8c84 NeedsCompilation: no Package: RTNduals Version: 1.22.0 Depends: R(>= 3.6.3), RTN(>= 2.14.1), methods Imports: graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 757ed534ffd05606d306b8f97d3f0868 NeedsCompilation: no Package: RTNsurvival Version: 1.22.0 Depends: R(>= 3.6.3), RTN(>= 2.14.1), RTNduals(>= 1.14.1), methods Imports: survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test Suggests: Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 07e60983480d0e6ca9c4cd034e0b34d9 NeedsCompilation: no Package: RTopper Version: 1.44.1 Depends: R (>= 2.12.0), Biobase Imports: limma, multtest Suggests: org.Hs.eg.db, KEGGREST, GO.db License: GPL (>= 3) + file LICENSE MD5sum: 6bf77abed8eb267c2e7c0ad7d6d5f3d8 NeedsCompilation: no Package: Rtpca Version: 1.8.0 Depends: R (>= 4.0.0), stats, dplyr, tidyr Imports: Biobase, methods, ggplot2, pROC, fdrtool, splines, utils, tibble Suggests: knitr, BiocStyle, TPP, testthat, rmarkdown License: GPL-3 MD5sum: c3428c44c312406599a5c76a589e78dc NeedsCompilation: no Package: rtracklayer Version: 1.58.0 Depends: R (>= 3.5.0), methods, GenomicRanges (>= 1.37.2) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.35.3), S4Vectors (>= 0.23.18), IRanges (>= 2.13.13), XVector (>= 0.19.7), GenomeInfoDb (>= 1.15.2), Biostrings (>= 2.47.6), zlibbioc, RCurl (>= 1.4-2), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), BiocIO, tools, restfulr (>= 0.0.13) LinkingTo: S4Vectors, IRanges, XVector Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit License: Artistic-2.0 + file LICENSE MD5sum: cc7175c537ed4a3007d2b34aa4b94078 NeedsCompilation: yes Package: Rtreemix Version: 1.60.0 Depends: R (>= 2.5.0) Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz License: LGPL MD5sum: 104d5e970842c5c547b00e5562760ecd NeedsCompilation: yes Package: rTRM Version: 1.36.0 Depends: R (>= 2.10), igraph (>= 1.0) Imports: methods, AnnotationDbi, DBI, RSQLite Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 34d53db5bbe458f222a39ce78d2196ed NeedsCompilation: no Package: rTRMui Version: 1.36.0 Imports: shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: f262362f2b2ad7bdba8dcaf5f92341f3 NeedsCompilation: no Package: runibic Version: 1.20.0 Depends: R (>= 3.4.0), biclust, SummarizedExperiment Imports: Rcpp (>= 0.12.12), testthat, methods LinkingTo: Rcpp Suggests: knitr, rmarkdown, GEOquery, affy, airway, QUBIC License: MIT + file LICENSE MD5sum: 33bd9363ccd2927a388dd1ac9e7fe555 NeedsCompilation: yes Package: RUVcorr Version: 1.30.0 Imports: corrplot, MASS, stats, lattice, grDevices, gridExtra, snowfall, psych, BiocParallel, grid, bladderbatch, reshape2, graphics Suggests: knitr, hgu133a2.db, rmarkdown License: GPL-2 MD5sum: 595e8b22a044dae0760130c9be28e474 NeedsCompilation: no Package: RUVnormalize Version: 1.32.0 Depends: R (>= 2.10.0) Imports: RUVnormalizeData, Biobase Enhances: spams License: GPL-3 MD5sum: 61e02f5e710c572ddaa8c252fb08f46b NeedsCompilation: no Package: RUVSeq Version: 1.32.0 Depends: Biobase, EDASeq (>= 1.99.1), edgeR Imports: methods, MASS Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 License: Artistic-2.0 MD5sum: 932b00f30b3650bc5d84d56bc4a228f3 NeedsCompilation: no Package: RVS Version: 1.20.0 Depends: R (>= 3.5.0) Imports: GENLIB, gRain, snpStats, kinship2, methods, stats, utils Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation License: GPL-2 MD5sum: 8593935963ecb3883df338330027ee8e NeedsCompilation: no Package: rWikiPathways Version: 1.18.2 Imports: httr, utils, XML, rjson, data.table, tidyr, RCurl Suggests: testthat, BiocStyle, knitr, rmarkdown, BridgeDbR License: MIT + file LICENSE MD5sum: d130a072bfe0977e6ba0c72b78678cfe NeedsCompilation: no Package: S4Vectors Version: 0.36.2 Depends: R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>= 0.37.0) Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 8404b1ea162990d9cccf7c7006805ad5 NeedsCompilation: yes Package: safe Version: 3.38.0 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: GPL (>= 2) MD5sum: 89af07f9b5bf46d97acf85ce113a8843 NeedsCompilation: no Package: sagenhaft Version: 1.68.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: ea8d4058b38bc8388a60bd17dfbb9cb8 NeedsCompilation: no Package: SAIGEgds Version: 1.12.5 Depends: R (>= 3.5.0), gdsfmt (>= 1.20.0), SeqArray (>= 1.31.8), Rcpp Imports: methods, stats, utils, RcppParallel, SPAtest (>= 3.0.0) LinkingTo: Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0) Suggests: parallel, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics, SNPRelate, ggmanh License: GPL-3 MD5sum: 8b05a27488d6dbf35b8c6546fdcea65e NeedsCompilation: yes Package: sampleClassifier Version: 1.22.0 Depends: R (>= 4.0), MGFM, MGFR, annotate Imports: e1071, ggplot2, stats, utils Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db License: Artistic-2.0 MD5sum: d02fde62b8e98212b364660f574f98d3 NeedsCompilation: no Package: SamSPECTRAL Version: 1.52.0 Depends: R (>= 3.3.3) Imports: methods License: GPL (>= 2) MD5sum: 8273c067cf19811dc6df104dc9381072 NeedsCompilation: yes Package: sangeranalyseR Version: 1.8.0 Depends: R (>= 4.0.0), stringr, ape, Biostrings, DECIPHER, parallel, reshape2, phangorn, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle, logger Suggests: testthat (>= 2.1.0) License: GPL-2 MD5sum: 28357bef24c268e3fb785a0cf5892949 NeedsCompilation: no Package: sangerseqR Version: 1.34.0 Depends: R (>= 3.0.2), Biostrings Imports: methods, shiny Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 MD5sum: bf4800712ffbeef61f60ae2df0b71533 NeedsCompilation: no Package: SANTA Version: 2.34.0 Depends: R (>= 4.1), igraph Imports: graphics, Matrix, methods, stats Suggests: BiocGenerics, BioNet, DLBCL, formatR, knitr, msm, org.Sc.sgd.db, markdown, rmarkdown, RUnit License: GPL (>= 2) MD5sum: 06e328d9fc0df2335639f7513b0e0a92 NeedsCompilation: yes Package: sarks Version: 1.10.0 Depends: R (>= 4.0) Imports: rJava, Biostrings, IRanges, utils, stats, cluster, binom Suggests: RUnit, BiocGenerics, ggplot2 License: BSD_3_clause + file LICENSE MD5sum: 0f9c54fbc3b40146633f981a1ead23d9 NeedsCompilation: no Package: satuRn Version: 1.6.0 Depends: R (>= 4.1) Imports: locfdr, SummarizedExperiment, BiocParallel, limma, pbapply, ggplot2, boot, Matrix, stats, methods, graphics Suggests: knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray License: Artistic-2.0 MD5sum: e17ff9c2780acf0e150510c519185bd9 NeedsCompilation: no Package: savR Version: 1.36.0 Depends: ggplot2 Imports: methods, reshape2, scales, gridExtra, XML Suggests: Cairo, testthat License: AGPL-3 MD5sum: 628e369b6055c8d7993a6a2ca4580b1f NeedsCompilation: no Package: SBGNview Version: 1.12.0 Depends: R (>= 3.6), pathview, SBGNview.data Imports: Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi, httr, KEGGREST, bookdown Suggests: testthat, gage License: AGPL-3 MD5sum: 2a2721414eb58d11e81d0330ca17cae5 NeedsCompilation: no Package: SBMLR Version: 1.94.0 Depends: XML, deSolve Suggests: rsbml License: GPL-2 MD5sum: ffac41d6dd902f2c065f1abac94d2671 NeedsCompilation: no Package: SC3 Version: 1.26.2 Depends: R(>= 3.3) Imports: graphics, stats, utils, methods, e1071, parallel, foreach, doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR, robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1), SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, mclust, scater License: GPL-3 MD5sum: 493d9d7064adf3fbe66f1eb266cf7c71 NeedsCompilation: yes Package: Scale4C Version: 1.20.0 Depends: R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: 9fe42c4d99dc78c9c4d45e64717e53c9 NeedsCompilation: no Package: ScaledMatrix Version: 1.6.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular License: GPL-3 MD5sum: 9c1086352d5749b4c27da04ca7530c08 NeedsCompilation: no Package: scAlign Version: 1.12.0 Depends: R (>= 3.6), SingleCellExperiment (>= 1.4), Seurat (>= 2.3.4), tensorflow, purrr, irlba, Rtsne, ggplot2, methods, utils, FNN Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 262b37c6fe85922c8770a2f87bfd10c4 NeedsCompilation: no Package: SCAN.UPC Version: 2.40.0 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva Imports: utils, methods, MASS, tools, IRanges Suggests: pd.hg.u95a License: MIT MD5sum: 11dce837faafc3d6488941f01647b95f NeedsCompilation: no Package: scanMiR Version: 1.4.0 Depends: R (>= 4.0) Imports: Biostrings, GenomicRanges, IRanges, data.table, BiocParallel, methods, GenomeInfoDb, S4Vectors, ggplot2, stats, stringi, utils, graphics, grid, ggseqlogo, cowplot Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 10c7b2b46c461f673dfb8fc51e8f1b86 NeedsCompilation: no Package: scanMiRApp Version: 1.4.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel, Biostrings, data.table, digest, DT, ensembldb, fst, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs, rtracklayer, S4Vectors, scanMiR, scanMiRData, shiny, shinycssloaders, shinydashboard, shinyjqui, stats, utils, waiter Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-3 MD5sum: a25f3f901dc236e49ff66f10d81cc6ad NeedsCompilation: no Package: scAnnotatR Version: 1.4.0 Depends: R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment Imports: dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, AnnotationHub, utils Suggests: knitr, rmarkdown, scRNAseq, testthat License: MIT + file LICENSE MD5sum: d9eb50d9e2d6ca4390e2524749a05073 NeedsCompilation: no Package: SCANVIS Version: 1.12.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file LICENSE MD5sum: c078206af574aa9ea18fb511118029a1 NeedsCompilation: no Package: SCArray Version: 1.6.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.27.4), methods, DelayedArray (>= 0.16.0) Imports: BiocGenerics, S4Vectors, IRanges, utils, SummarizedExperiment, SingleCellExperiment, DelayedMatrixStats Suggests: Matrix, scater, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array License: GPL-3 MD5sum: bb0483dd6621792829b6f738f88cee74 NeedsCompilation: yes Package: SCATE Version: 1.8.0 Depends: parallel, preprocessCore, splines, splines2, xgboost, SCATEData, Rtsne, mclust Imports: utils, stats, GenomicAlignments, GenomicRanges Suggests: rmarkdown, ggplot2, knitr License: MIT + file LICENSE MD5sum: 29e007e8c886e37e62af26fc3267e20f NeedsCompilation: no Package: scater Version: 1.26.1 Depends: SingleCellExperiment, scuttle, ggplot2 Imports: stats, utils, methods, grid, gridExtra, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer, RcppML, uwot, pheatmap, ggrastr, ggrepel Suggests: BiocStyle, snifter, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase License: GPL-3 MD5sum: 49a00d8296149e57f67e5d12856c1289 NeedsCompilation: no Package: scatterHatch Version: 1.4.0 Depends: R (>= 4.1) Imports: grid, ggplot2, plyr, spatstat.geom, stats, grDevices Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 4850280493256b81c291984068018c24 NeedsCompilation: no Package: scBFA Version: 1.12.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods, Matrix Suggests: knitr, rmarkdown, testthat, Rtsne License: GPL-3 + file LICENSE MD5sum: 25e6092c94496ee9fac7f79cfd649202 NeedsCompilation: no Package: SCBN Version: 1.16.0 Depends: R (>= 3.5.0) Imports: stats Suggests: knitr,rmarkdown License: GPL-2 MD5sum: ed522c3ece872f6319cde92a9f972689 NeedsCompilation: no Package: scBubbletree Version: 1.0.0 Depends: R (>= 4.2.0) Imports: reshape2, future, future.apply, ape, scales, Seurat, ggplot2, ggtree, patchwork, methods, stats, base, utils Suggests: BiocStyle, knitr, testthat, cluster, SingleCellExperiment License: GPL-3 + file LICENSE MD5sum: 7a2c3b3070f5d5b4badf7544f155f087 NeedsCompilation: no Package: scCB2 Version: 1.8.0 Depends: R (>= 3.6.0) Imports: SingleCellExperiment, SummarizedExperiment, Matrix, methods, utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel, iterators, foreach, Seurat Suggests: testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 7512414d449023981782f36e41b20cca NeedsCompilation: yes Package: scClassify Version: 1.10.0 Depends: R (>= 4.0) Imports: S4Vectors, limma, ggraph, igraph, methods, cluster, minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix, ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo Suggests: knitr, rmarkdown, BiocStyle, pkgdown License: GPL-3 MD5sum: 011aa5058d6ebafd4f6e63a5deb383be NeedsCompilation: no Package: sccomp Version: 1.2.1 Depends: R (>= 4.2.0) Imports: methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstantools (>= 2.1.1), rstan (>= 2.18.1), SeuratObject, SingleCellExperiment, parallel, dplyr, tidyr, purrr, magrittr, rlang, tibble, boot, lifecycle, stats, tidyselect, utils, ggplot2, ggrepel, patchwork, forcats, readr, scales, stringr, glue LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, testthat (>= 3.0.0), markdown, knitr, tidyseurat, tidySingleCellExperiment, loo Enhances: furrr, extraDistr License: GPL-3 MD5sum: f862c79ca0c15cb775b6bda2f7920691 NeedsCompilation: yes Package: scDataviz Version: 1.8.0 Depends: R (>= 4.0), S4Vectors, SingleCellExperiment, Imports: ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales, RColorBrewer, corrplot, stats, grDevices, graphics, utils, MASS, matrixStats, methods Suggests: PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: dbbddacb255aafef43492da777322d9f NeedsCompilation: no Package: scDblFinder Version: 1.12.0 Depends: R (>= 4.0), SingleCellExperiment Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost, stats, utils, MASS, IRanges, GenomicRanges, GenomeInfoDb, Rsamtools, rtracklayer Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans License: GPL-3 + file LICENSE MD5sum: b1131cba5b79264700f26ca27be0292b NeedsCompilation: no Package: scDD Version: 1.22.0 Depends: R (>= 3.5.0) Imports: fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm, SingleCellExperiment, SummarizedExperiment, grDevices, graphics, stats, S4Vectors, scran Suggests: BiocStyle, knitr, gridExtra License: GPL-2 MD5sum: 43ddf42535a11a193b5d9b23bf2318d2 NeedsCompilation: yes Package: scDDboost Version: 1.0.0 Depends: R (>= 4.2), ggplot2 Imports: Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0),EBSeq, BiocParallel, mclust, SingleCellExperiment, cluster, Oscope, SummarizedExperiment, stats, methods LinkingTo: Rcpp, RcppEigen, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: f45ffa21932575f85e7eabdb5ac8a408 NeedsCompilation: yes Package: scde Version: 2.26.2 Depends: R (>= 3.0.0), flexmix Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown License: GPL-2 MD5sum: 08f7ffee4de2317b30823c07ade97315 NeedsCompilation: yes Package: scds Version: 1.14.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown License: MIT + file LICENSE MD5sum: a03841ee30fc0e770e5b00ae5ab0ca48 NeedsCompilation: no Package: SCFA Version: 1.8.1 Depends: R (>= 4.0) Imports: matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph, Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival Suggests: knitr, rmarkdown License: LGPL MD5sum: f3fef0cc4f91c417d83bb6f8919f54a0 NeedsCompilation: no Package: scFeatureFilter Version: 1.18.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods Suggests: testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE MD5sum: f5324716544954dae085d0d673a9812a NeedsCompilation: no Package: scGPS Version: 1.12.2 Depends: R (>= 3.6), SummarizedExperiment, dynamicTreeCut, SingleCellExperiment Imports: glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1), fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel, grDevices, graphics, stats, utils, DESeq2, locfit LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE License: GPL-3 MD5sum: 2c7a83f471ed12aca1874d626d3f8d71 NeedsCompilation: yes Package: schex Version: 1.12.0 Depends: SingleCellExperiment (>= 1.7.4), Seurat, ggplot2 (>= 3.2.1), shiny Imports: hexbin, stats, methods, cluster, dplyr, entropy, ggforce, scales, grid, concaveman Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran License: GPL-3 MD5sum: cf21f9642b8d321c946f98defb64cf94 NeedsCompilation: no Package: scHOT Version: 1.10.0 Depends: R (>= 4.0) Imports: S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix, SummarizedExperiment, IRanges, methods, stats, BiocParallel, reshape, ggplot2, igraph, grDevices, ggforce, graphics Suggests: knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir License: GPL-3 MD5sum: 90d5dc43bcaf662e97857e14ccd3ab32 NeedsCompilation: no Package: scifer Version: 1.0.0 Imports: dplyr, rmarkdown, data.table, Biostrings, parallel, stats, plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra, tibble, scales, rlang, flowCore, methods Suggests: fs, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: bad38f6d75de43e08a89a6e2236ab9e0 NeedsCompilation: no Package: scMAGeCK Version: 1.9.1 Imports: Seurat, ggplot2, stats, utils Suggests: knitr, rmarkdown License: BSD_2_clause MD5sum: 7b21647e40a871924025b9a0276c4055 NeedsCompilation: yes Package: scmap Version: 1.20.2 Depends: R(>= 3.4) Imports: Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 0a19b50a0a8a65ca5595d35f948e7068 NeedsCompilation: yes Package: scMerge Version: 1.14.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), parallel, pdist, proxy, ruv, S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3), SummarizedExperiment Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, scater, testthat, badger License: GPL-3 MD5sum: 9c5d99f5cf8e4a48806ef4b7a08ffa42 NeedsCompilation: no Package: scMET Version: 1.0.0 Depends: R (>= 4.2.0) Imports: methods, Rcpp (>= 1.0.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), rstantools (>= 2.1.0), VGAM, data.table, MASS, logitnorm, ggplot2, matrixStats, assertthat, viridis, coda, BiocStyle, cowplot, stats, SummarizedExperiment, SingleCellExperiment, Matrix, dplyr, S4Vectors LinkingTo: BH (>= 1.66.0), Rcpp (>= 1.0.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), StanHeaders (>= 2.21.0.7) Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 2624cfeecb7e2d55bae3b55dc0dda8db NeedsCompilation: yes Package: scmeth Version: 1.18.0 Depends: R (>= 3.5.0) Imports: knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes License: GPL-2 MD5sum: eb0171295587fe6dc4bc25af138dffd9 NeedsCompilation: no Package: SCnorm Version: 1.20.0 Depends: R (>= 3.4.0), Imports: SingleCellExperiment, SummarizedExperiment, stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, S4Vectors, ggplot2, forcats, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) MD5sum: d9cf4f2fbf010dd0a173afefb500f2ab NeedsCompilation: no Package: scone Version: 1.22.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, BatchJobs, splatter, scater, kableExtra, mclust, TENxPBMCData License: Artistic-2.0 MD5sum: 1a27594985a8cb4d3ee3fbab10314d7c NeedsCompilation: no Package: Sconify Version: 1.18.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 19d32efc62e19da1cf84ac13e09601ac NeedsCompilation: no Package: SCOPE Version: 1.10.0 Depends: R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19 Imports: stats, grDevices, graphics, utils, DescTools, RColorBrewer, gplots, foreach, parallel, doParallel, DNAcopy, BSgenome, Biostrings, BiocGenerics, S4Vectors Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) License: GPL-2 MD5sum: 30a18e783f11ea81a32b7932eb73a6ee NeedsCompilation: no Package: scoreInvHap Version: 1.20.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: 7b61266950c4d1412f7be40bd7b8a458 NeedsCompilation: no Package: scp Version: 1.8.0 Depends: R (>= 4.2.0), QFeatures (>= 1.3.5) Imports: methods, stats, utils, SingleCellExperiment, SummarizedExperiment, MultiAssayExperiment, MsCoreUtils, matrixStats, S4Vectors, dplyr, magrittr Suggests: testthat, knitr, BiocStyle, rmarkdown, patchwork, ggplot2, impute, scater, sva, preprocessCore, vsn, uwot License: Artistic-2.0 MD5sum: 185713450361774c0a087d040c56697a NeedsCompilation: no Package: scPCA Version: 1.12.0 Depends: R (>= 4.0.0) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca, cluster, kernlab, origami, RSpectra, coop, Matrix, DelayedArray, ScaledMatrix, MatrixGenerics Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark License: MIT + file LICENSE MD5sum: f1fc3d6e40ac424f090787892359ed1c NeedsCompilation: no Package: scPipe Version: 1.20.6 Depends: R (>= 4.2.0), SingleCellExperiment Imports: AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings, data.table, dplyr, DropletUtils, flexmix, GenomicRanges, GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grDevices, graphics, hash, IRanges, magrittr, MASS, Matrix (>= 1.5.0), mclust, methods, MultiAssayExperiment, org.Hs.eg.db, org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate, Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer, SummarizedExperiment, S4Vectors, scales, stats, stringr, tibble, tidyr, tools, utils, LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap License: GPL (>= 2) MD5sum: 18ab2ad1a40f3b2653b6f63f1a41c38e NeedsCompilation: yes Package: scran Version: 1.26.2 Depends: SingleCellExperiment, scuttle Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, bluster, metapod, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, monocle, Biobase, pheatmap, scater License: GPL-3 MD5sum: b75ee89e2df29916dfe93c06861bd160 NeedsCompilation: yes Package: scReClassify Version: 1.4.0 Depends: R (>= 4.1) Imports: randomForest, e1071, stats, SummarizedExperiment, SingleCellExperiment, methods Suggests: testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr License: GPL-3 + file LICENSE MD5sum: 1667b94f560ceec6975c8c8a20919eda NeedsCompilation: no Package: scRecover Version: 1.14.1 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL MD5sum: 93001b9271a8167d75cb6b759a3a9bb6 NeedsCompilation: no Package: ScreenR Version: 1.0.0 Depends: R (>= 4.2) Imports: methods (>= 4.0), rlang (>= 0.4), stringr (>= 1.4), limma (>= 3.46), patchwork (>= 1.1), tibble (>= 3.1.6), scales (>= 1.1.1), ggvenn (>= 0.1.9), purrr (>= 0.3.4), ggplot2 (>= 3.3), stats, tidyr (>= 1.2), magrittr (>= 1.0), dplyr (>= 1.0), edgeR (>= 3.32), tidyselect (>= 1.1.2) Suggests: rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0), BiocStyle (>= 2.22.0), covr (>= 3.5) License: MIT + file LICENSE MD5sum: f47489699de0e17251ed8253deef5ffb NeedsCompilation: no Package: scRepertoire Version: 1.8.0 Depends: ggplot2, R (>= 4.0) Imports: stringdist, dplyr, reshape2, ggalluvial, stringr, vegan, powerTCR, SingleCellExperiment, SummarizedExperiment, plyr, parallel, doParallel, methods, utils, rlang, igraph, ggraph, tidygraph, SeuratObject Suggests: knitr, rmarkdown, BiocStyle, circlize, scales, Seurat, scater License: GPL-2 MD5sum: 390b786725eb6e85d55d6b53fbc90092 NeedsCompilation: no Package: scruff Version: 1.16.0 Depends: R (>= 4.0) Imports: data.table, GenomicAlignments, GenomicFeatures, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: f6cc681e4b17304cabb5588bd717daeb NeedsCompilation: no Package: scry Version: 1.10.0 Depends: R (>= 4.0), stats, methods Imports: DelayedArray, glmpca (>= 0.2.0), HDF5Array, Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular Suggests: markdown, BiocGenerics, covr, DuoClustering2018, ggplot2, knitr, rmarkdown, TENxPBMCData, testthat License: Artistic-2.0 MD5sum: c9aa38d89dd8f2ed22d68b444ab4fe49 NeedsCompilation: no Package: scShapes Version: 1.4.0 Depends: R (>= 4.1) Imports: Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS, emdbook, magrittr, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 5c6e4b1c85855eece061f9db8b0902db NeedsCompilation: yes Package: scTensor Version: 2.8.0 Depends: R (>= 4.1.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8), abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics, stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2 Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens License: Artistic-2.0 MD5sum: 1d9aac945bfe75794f8eb6778cdcee23 NeedsCompilation: no Package: scTGIF Version: 1.12.0 Depends: R (>= 3.6.0) Imports: GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly, tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr, S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor, methods, scales, msigdbr, schex, tibble, ggplot2, igraph Suggests: testthat License: Artistic-2.0 MD5sum: aa3fb4222a640c7ef58b6135ff4163c8 NeedsCompilation: no Package: scTHI Version: 1.10.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown License: GPL-2 MD5sum: 37be49390b4d0b017204a350cbb6bcee NeedsCompilation: no Package: scTreeViz Version: 1.4.0 Depends: R (>= 4.0), methods, epivizr, SummarizedExperiment Imports: data.table, S4Vectors, digest, Matrix, Rtsne, httr, igraph, clustree, scran, sys, epivizrData, epivizrServer, ggraph, scater, Seurat, SingleCellExperiment, ggplot2, stats, utils Suggests: knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb License: Artistic-2.0 MD5sum: dbc0c09c7df3c30b7469ad195ed5697e NeedsCompilation: no Package: scuttle Version: 1.8.4 Depends: SingleCellExperiment Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran License: GPL-3 MD5sum: d3809c66c36cadd0be0ab8a7070fbbbc NeedsCompilation: yes Package: SDAMS Version: 1.18.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: 26931c63b22d09333f3162665d260617 NeedsCompilation: no Package: sechm Version: 1.6.0 Depends: R (>= 4.0) Imports: S4Vectors, SummarizedExperiment, seriation, ComplexHeatmap, circlize, methods, randomcoloR, stats, grid, grDevices, matrixStats Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 3ec4df827db4129275a8782e806d1f24 NeedsCompilation: no Package: segmenter Version: 1.4.0 Depends: R (>= 4.1) Imports: ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges, S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils, methods, chromhmmData Suggests: testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz License: GPL-3 MD5sum: ae36cdc0da8a3592632abcaa3654a66f NeedsCompilation: no Package: segmentSeq Version: 2.32.0 Depends: R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: 037157695e46d02bd8d08a675432fea6 NeedsCompilation: no Package: selectKSigs Version: 1.10.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: 7d3257cd0a511c5fb850296e773f3141 NeedsCompilation: yes Package: SELEX Version: 1.30.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: d2a0d577241fb483771537befa65ffc2 NeedsCompilation: no Package: SemDist Version: 1.32.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) MD5sum: 27cd2f1337d1af51aad1684bcdddefa8 NeedsCompilation: no Package: semisup Version: 1.22.0 Depends: R (>= 3.0.0) Imports: VGAM Suggests: knitr, testthat, SummarizedExperiment License: GPL-3 MD5sum: a71ff9963ae3472e35ca4e0d8eb7e606 NeedsCompilation: no Package: SEPIRA Version: 1.18.0 Depends: R (>= 3.5.0) Imports: limma (>= 3.32.5), corpcor (>= 1.6.9), parallel (>= 3.3.1), stats Suggests: knitr, rmarkdown, testthat, igraph License: GPL-3 MD5sum: 9dcc9607f7cfb5109e20a1bbdbe02dc0 NeedsCompilation: no Package: seq2pathway Version: 1.30.0 Depends: R (>= 3.6.2) Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data License: GPL-2 MD5sum: 4aa3b314396ba6711f18d933a55399ad NeedsCompilation: no Package: seqArchR Version: 1.2.0 Depends: R (>= 4.2.0) Imports: utils, graphics, cvTools (>= 0.3.2), MASS, Matrix, methods, stats, cluster, matrixStats, fpc, cli, prettyunits, reshape2 (>= 1.4.3), reticulate (>= 1.22), BiocParallel, Biostrings, grDevices, ggplot2 (>= 3.1.1), ggseqlogo (>= 0.1) Suggests: cowplot, hopach (>= 2.42.0), BiocStyle, knitr (>= 1.22), rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>= 0.3.0) License: GPL-3 | file LICENSE MD5sum: 216a3a6ab91a3233799935f0d1b17b90 NeedsCompilation: no Package: SeqArray Version: 1.38.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.31.1) Imports: methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors LinkingTo: gdsfmt Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation License: GPL-3 MD5sum: 57a086f0b8eed10c74c6827317acf435 NeedsCompilation: yes Package: seqbias Version: 1.46.0 Depends: R (>= 3.0.2), GenomicRanges (>= 0.1.0), Biostrings (>= 2.15.0), methods LinkingTo: Rhtslib (>= 1.99.1), zlibbioc Suggests: Rsamtools, ggplot2 License: LGPL-3 MD5sum: c05c07af008352e3fc607d7a56e3d244 NeedsCompilation: yes Package: seqCAT Version: 1.20.0 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE MD5sum: 289f0b1f46c9064d7c8df8d7672d36e3 NeedsCompilation: no Package: seqCNA Version: 1.44.0 Depends: R (>= 3.0), GLAD (>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot (>= 0.99), methods License: GPL-3 MD5sum: 6cdcf1f5c32255102ec548b6ec2d776b NeedsCompilation: yes Package: seqcombo Version: 1.20.0 Depends: R (>= 3.4.0) Imports: ggplot2, grid, igraph, utils, yulab.utils Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble License: Artistic-2.0 MD5sum: a6e363f154d0ce8d97c4e727c3723e93 NeedsCompilation: no Package: SeqGate Version: 1.8.0 Depends: S4Vectors, SummarizedExperiment, GenomicRanges Imports: stats, methods, BiocManager Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown License: GPL (>= 2.0) MD5sum: f16cc2c91e276bd114fdb81f3255f3e5 NeedsCompilation: no Package: SeqGSEA Version: 1.38.0 Depends: Biobase, doParallel, DESeq2 Imports: methods, biomaRt Suggests: GenomicRanges License: GPL (>= 3) MD5sum: 96a83a79d46b81e802608b90558dd304 NeedsCompilation: no Package: seqLogo Version: 1.64.0 Depends: R (>= 4.2), methods, grid Imports: stats4, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: LGPL (>= 2) MD5sum: efcf7a417a5d90b0fd0c95592e6863bd NeedsCompilation: no Package: seqPattern Version: 1.30.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 MD5sum: 46c57ea8690e017bf1e3ce733005e575 NeedsCompilation: no Package: seqsetvis Version: 1.18.1 Depends: R (>= 3.6), ggplot2 Imports: cowplot, data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, ggplotify, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, stats, UpSetR Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: d7769aba44dee5c85ecb4f2f11c4d6eb NeedsCompilation: no Package: SeqSQC Version: 1.20.0 Depends: R (>= 3.4), ExperimentHub (>= 1.3.7), SNPRelate (>= 1.10.2) Imports: e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, rbokeh, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: f724a66f473370cafcd4e06b1cf0b09f NeedsCompilation: no Package: seqTools Version: 1.32.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 260b5048afadb964a34c70c62428132b NeedsCompilation: yes Package: SeqVarTools Version: 1.36.0 Depends: SeqArray Imports: grDevices, graphics, stats, methods, Biobase, BiocGenerics, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, data.table, Suggests: BiocStyle, RUnit, stringr License: GPL-3 MD5sum: a702db8f540a1c474f51a3b42c316333 NeedsCompilation: no Package: sesame Version: 1.16.1 Depends: R (>= 4.1), sesameData Imports: graphics, BiocParallel, utils, methods, stringr, readr, tibble, illuminaio, MASS, wheatmap (>= 0.2.0), GenomicRanges, IRanges, grid, preprocessCore, S4Vectors, ggplot2, BiocFileCache, GenomeInfoDb, stats, SummarizedExperiment, dplyr, reshape2 Suggests: scales, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, pals License: MIT + file LICENSE MD5sum: 2f9a62f9dd05a24dfb095f3be153f6db NeedsCompilation: no Package: SEtools Version: 1.12.0 Depends: R (>= 4.0), SummarizedExperiment, sechm Imports: BiocParallel, Matrix, DESeq2, S4Vectors, data.table, edgeR, openxlsx, pheatmap, stats, circlize, methods, sva Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL MD5sum: dbef07a3d593da625756c8440af9adef NeedsCompilation: no Package: sevenbridges Version: 1.28.0 Depends: methods, utils, stats Imports: httr, jsonlite, yaml, objectProperties, stringr, S4Vectors, docopt, curl, uuid, data.table Suggests: knitr, rmarkdown, testthat, readr License: Apache License 2.0 | file LICENSE MD5sum: 0c8045e1c3140d54ba2d925bf800688a NeedsCompilation: no Package: sevenC Version: 1.18.0 Depends: R (>= 3.5), InteractionSet (>= 1.2.0) Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), GenomeInfoDb (>= 1.12.2), GenomicRanges (>= 1.28.5), IRanges (>= 2.10.3), S4Vectors (>= 0.14.4), readr (>= 1.1.0), purrr (>= 0.2.2), data.table (>= 1.10.4), boot (>= 1.3-20), methods (>= 3.4.1) Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr License: GPL-3 MD5sum: f3f755be4ac6d6344098381ca17ee684 NeedsCompilation: no Package: SGSeq Version: 1.32.0 Depends: R (>= 4.0), IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), Rsamtools (>= 1.31.2), SummarizedExperiment, methods Imports: AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>= 2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>= 1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19), grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7), stats Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown License: Artistic-2.0 MD5sum: 69df298bdaef5d928d8707834bb6634d NeedsCompilation: no Package: SharedObject Version: 1.12.0 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, Rcpp Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: cb2be5123174af25cf69b6aa93024a45 NeedsCompilation: yes Package: shinyepico Version: 1.6.0 Depends: R (>= 4.2.0) Imports: DT (>= 0.15.0), data.table (>= 1.13.0), doParallel (>= 1.0.0), dplyr (>= 1.0.9), foreach (>= 1.5.0), GenomicRanges (>= 1.38.0), ggplot2 (>= 3.3.0), gplots (>= 3.0.0), heatmaply (>= 1.1.0), limma (>= 3.42.0), minfi (>= 1.32.0), plotly (>= 4.9.2), reshape2 (>= 1.4.0), rlang (>= 1.0.2), rmarkdown (>= 2.3.0), rtracklayer (>= 1.46.0), shiny (>= 1.5.0), shinyWidgets (>= 0.5.0), shinycssloaders (>= 0.3.0), shinyjs (>= 1.1.0), shinythemes (>= 1.1.0), statmod (>= 1.4.0), tidyr (>= 1.2.0), zip (>= 2.1.0) Suggests: knitr (>= 1.30.0), mCSEA (>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData License: AGPL-3 + file LICENSE MD5sum: 8acfb6722b5372cc5d0fa87f58be7ef9 NeedsCompilation: no Package: shinyMethyl Version: 1.34.0 Depends: methods, BiocGenerics (>= 0.3.2), shiny (>= 0.13.2), minfi (>= 1.18.2), IlluminaHumanMethylation450kmanifest, matrixStats, R (>= 3.0.0) Imports: RColorBrewer Suggests: shinyMethylData, minfiData, BiocStyle, RUnit, digest, knitr License: Artistic-2.0 MD5sum: b766e3a4181e56a57e6ce2e207b87cc7 NeedsCompilation: no Package: ShortRead Version: 1.56.1 Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), hwriter, methods, zlibbioc, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi License: Artistic-2.0 MD5sum: c540e3fc6e7149e6f5e7e9e92657b690 NeedsCompilation: yes Package: SIAMCAT Version: 2.2.0 Depends: R (>= 3.6.0), mlr3, phyloseq Imports: beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot, lmerTest, mlr3learners, mlr3tuning, paradox, lgr Suggests: BiocStyle, optparse, testthat, knitr, rmarkdown, tidyverse, ggpubr License: GPL-3 MD5sum: df0a8586b2193f669fbf1858ba2bd52c NeedsCompilation: no Package: SICtools Version: 1.28.0 Depends: R (>= 3.0.0), methods, Rsamtools (>= 1.18.1), doParallel (>= 1.0.8), Biostrings (>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges (>= 1.22.4), IRanges (>= 2.4.8) Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: b09ae746a71f43735e7d96e526d5bfd4 NeedsCompilation: yes Package: SigCheck Version: 2.30.0 Depends: R (>= 3.2.0), MLInterfaces, Biobase, e1071, BiocParallel, survival Imports: graphics, stats, utils, methods Suggests: BiocStyle, breastCancerNKI, qusage License: Artistic-2.0 MD5sum: 0b13d6bf76771429417ec8bc170f4beb NeedsCompilation: no Package: sigFeature Version: 1.16.0 Depends: R (>= 3.5.0) Imports: biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer, Matrix, SparseM, graphics, stats, utils, SummarizedExperiment, BiocParallel, methods Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL (>= 2) MD5sum: 7020610a8e78b929b07b0cb374f95910 NeedsCompilation: no Package: SigFuge Version: 1.36.0 Depends: R (>= 3.5.0), GenomicRanges Imports: ggplot2, matlab, reshape, sigclust Suggests: org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle License: GPL-3 MD5sum: 6ab3ff4d834264895d655fa22ee881af NeedsCompilation: no Package: siggenes Version: 1.72.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: b86e037261fa175b95e97adc1f975ed5 NeedsCompilation: no Package: sights Version: 1.24.0 Depends: R(>= 3.3) Imports: MASS(>= 7.3), qvalue(>= 2.2), ggplot2(>= 2.0), reshape2(>= 1.4), lattice(>= 0.2), stats(>= 3.3) Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx License: GPL-3 | file LICENSE MD5sum: 1ecdb67af4330d0b22f1f422f43915f5 NeedsCompilation: no Package: signatureSearch Version: 1.12.0 Depends: R(>= 3.6.0), Rcpp, SummarizedExperiment, org.Hs.eg.db Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, utils, reshape2, visNetwork, BiocParallel, fastmatch, reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray, BiocGenerics, tibble LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT License: Artistic-2.0 MD5sum: 72eaddcbc4cca49c4adf898038baa655 NeedsCompilation: yes Package: signeR Version: 2.0.2 Depends: R (>= 3.0.2), VariantAnnotation, NMF Imports: BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat, survivalAnalysis, future, VGAM, MASS, kknn, glmnet, e1071, randomForest, ada, future.apply, ggplot2, pROC, pheatmap, RColorBrewer, listenv, reshape2, scales, survminer, dplyr, ggpubr, cowplot, tibble, readr, shiny, shinydashboard, shinycssloaders, shinyWidgets, bsplus, DT, magrittr, tidyr, BiocFileCache, proxy, rtracklayer, BSgenome LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown License: GPL-3 MD5sum: bbb24d15e170e57b7afe5c8ee126bff3 NeedsCompilation: yes Package: signifinder Version: 1.0.0 Depends: R (>= 4.2.0) Imports: ggplot2, org.Hs.eg.db, patchwork, AnnotationDbi, BiocGenerics, ComplexHeatmap, DGEobj.utils, GSVA, IRanges, SummarizedExperiment, consensusOV, dplyr, ensembldb, ggridges, grid, magrittr, matrixStats, maxstat, methods, openair, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, stats, survival, survminer, viridis Suggests: BiocStyle, knitr, kableExtra, testthat (>= 3.0.0), edgeR, limma License: AGPL-3 MD5sum: 79344378bc2d1b725a80158968cca848 NeedsCompilation: no Package: sigPathway Version: 1.66.2 Depends: R (>= 2.10) Suggests: hgu133a.db (>= 1.10.0), XML (>= 1.6-3), AnnotationDbi (>= 1.3.12) License: GPL-2 MD5sum: 2a063d125b5ac8f69ad1cd13c5b86d13 NeedsCompilation: yes Package: SigsPack Version: 1.12.0 Depends: R (>= 3.6) Imports: quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0), VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb, GenomicRanges, rtracklayer, SummarizedExperiment, graphics, stats, utils Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: dcf329d886a27d34206abc243be95cf8 NeedsCompilation: no Package: sigsquared Version: 1.30.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 4b13729de70197838016b770bacb7ef8 NeedsCompilation: no Package: SIM Version: 1.68.0 Depends: R (>= 3.5), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) MD5sum: f96c6bb3a1580c4c2b4fd0d8f701df56 NeedsCompilation: yes Package: SIMAT Version: 1.30.0 Depends: R (>= 3.5.0), Rcpp (>= 0.11.3) Imports: mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 965a2757e4c4be8a641c9f215568b3b7 NeedsCompilation: no Package: SimBindProfiles Version: 1.36.0 Depends: R (>= 2.10), methods, Ringo Imports: limma, mclust, Biobase License: GPL-3 MD5sum: f81a5be31f0a554f56e83a353f4979fc NeedsCompilation: no Package: SimBu Version: 1.0.2 Imports: basilisk, BiocParallel, data.table, dplyr, ggplot2, tools, Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer, RCurl, reticulate, sparseMatrixStats, SummarizedExperiment, tidyr Suggests: curl, knitr, matrixStats, rmarkdown, Seurat, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: b4694a3eb954fb32f0f230e2b026d969 NeedsCompilation: no Package: SIMD Version: 1.16.0 Depends: R (>= 3.5.0) Imports: edgeR, statmod, methylMnM, stats, utils Suggests: BiocStyle, knitr,rmarkdown License: GPL-3 MD5sum: f4e2cfcbc6b5d2dc94dcdc5110d7fcec NeedsCompilation: yes Package: SimFFPE Version: 1.10.0 Depends: Biostrings Imports: dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods Suggests: BiocStyle License: LGPL-3 MD5sum: 5a6f64695c7d778346c73e54c7ed020c NeedsCompilation: no Package: similaRpeak Version: 1.30.0 Depends: R6 (>= 2.0) Imports: stats Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 4e89e7d64ec8640c7d47cb4a84d5e643 NeedsCompilation: no Package: SIMLR Version: 1.24.3 Depends: R (>= 4.1.0), Imports: parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra LinkingTo: Rcpp Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph License: file LICENSE MD5sum: cacc35ba6d18104a7f63ead0a76a327c NeedsCompilation: yes Package: simpleSeg Version: 1.0.2 Depends: R (>= 3.5.0) Imports: BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors, grDevices, SummarizedExperiment, methods, cytomapper Suggests: BiocStyle, testthat (>= 3.0.0), knitr, ggplot2 License: GPL-3 MD5sum: b34a6f9d422a3a22d7a7dc815f6165ab NeedsCompilation: no Package: simplifyEnrichment Version: 1.8.0 Depends: R (>= 3.6.0), BiocGenerics, grid Imports: GOSemSim, ComplexHeatmap (>= 2.7.4), circlize, GetoptLong, digest, tm, GO.db, org.Hs.eg.db, AnnotationDbi, slam, methods, clue, grDevices, graphics, stats, utils, proxyC, Matrix, cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0) Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, clusterProfiler, msigdbr, DOSE, DO.db, reactome.db, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc License: MIT + file LICENSE MD5sum: 8ddf553a7dc8af6931d516c2c69ed531 NeedsCompilation: no Package: sincell Version: 1.30.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: GPL (>= 2) MD5sum: 21d3113e56315d430122b929f5e048ba NeedsCompilation: yes Package: single Version: 1.2.0 Depends: R (>= 4.1) Imports: Biostrings, BiocGenerics, dplyr, GenomicAlignments,IRanges, methods, reshape2, rlang, Rsamtools, stats, stringr, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 9bbf3d7d882225ff5caebd8e273a5509 NeedsCompilation: no Package: SingleCellExperiment Version: 1.20.1 Depends: SummarizedExperiment Imports: methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne License: GPL-3 MD5sum: 5ecee11cc8266a5bb34cab7277dcc43b NeedsCompilation: no Package: SingleCellSignalR Version: 1.10.0 Depends: R (>= 4.0) Imports: BiocManager, circlize, limma, igraph, gplots, grDevices, edgeR, SIMLR, data.table, pheatmap, stats, Rtsne, graphics, stringr, foreach, multtest, scran, utils, Suggests: knitr, rmarkdown License: GPL-3 MD5sum: b0f12e269ca633d0834b368283418346 NeedsCompilation: no Package: singleCellTK Version: 2.8.0 Depends: R (>= 4.0), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase Imports: ape, AnnotationHub, batchelor, BiocParallel, celldex, colourpicker, colorspace, cowplot, cluster, ComplexHeatmap, data.table, DelayedMatrixStats, DESeq2, dplyr, DT, ExperimentHub, ensembldb, fields, ggplot2, ggplotify, ggrepel, ggtree, gridExtra, GSVA (>= 1.26.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix, matrixStats, methods, msigdbr, multtest, plotly, plyr, ROCR, Rtsne, S4Vectors, scater, scMerge (>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, SoupX, sva, reshape2, shinyalert, circlize, enrichR, celda, shinycssloaders, DropletUtils, scds (>= 1.2.0), reticulate (>= 1.14), tools, tximport, fishpond, withr, GSEABase, R.utils, zinbwave, scRNAseq (>= 2.0.2), TENxPBMCData, yaml, rmarkdown, magrittr, scDblFinder, metap, VAM (>= 0.5.3), tibble, rlang, TSCAN, TrajectoryUtils, scuttle, utils, stats Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony License: MIT + file LICENSE MD5sum: ec3251341ebd3c2f0c3d53b8392e5dc2 NeedsCompilation: no Package: SingleMoleculeFootprinting Version: 1.6.0 Depends: R (>= 4.1.0) Imports: BiocGenerics, Biostrings, BSgenome, GenomeInfoDb, GenomicRanges, data.table, grDevices, plyr, IRanges, RColorBrewer, stats, QuasR Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, parallel, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0) License: GPL-3 MD5sum: 9b30f188aa5f2869010d021d039c0957 NeedsCompilation: no Package: SingleR Version: 2.0.0 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocSingular, stats, utils, Rcpp, beachmat, parallel LinkingTo: Rcpp, beachmat, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scater, scran, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 + file LICENSE MD5sum: 920b6479bf660e746983697893524cd0 NeedsCompilation: yes Package: singscore Version: 1.18.0 Depends: R (>= 3.6) Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, reshape2, S4Vectors Suggests: pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: 9bcae0cc8d8f939786e49fe16e2cf916 NeedsCompilation: no Package: SISPA Version: 1.28.0 Depends: R (>= 3.5),genefilter,GSVA,changepoint Imports: data.table, plyr, ggplot2 Suggests: knitr License: GPL-2 MD5sum: e9ca2b44074eb99bb9324ba0db3fb35c NeedsCompilation: no Package: sitadela Version: 1.6.0 Depends: R (>= 4.1.0) Imports: Biobase, BiocGenerics, biomaRt, Biostrings, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, methods, parallel, Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, utils Suggests: BSgenome, knitr, rmarkdown, RMySQL, RUnit License: Artistic-2.0 MD5sum: db368b2865c63bd6e0bfcada9ae3a75a NeedsCompilation: no Package: sitePath Version: 1.14.0 Depends: R (>= 4.1) Imports: RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree, graphics, grDevices, gridExtra, methods, parallel, seqinr, stats, tidytree, utils LinkingTo: Rcpp Suggests: BiocStyle, devtools, knitr, magick, rmarkdown, testthat License: MIT + file LICENSE MD5sum: b4439e3d7f9b7b398398d33572546508 NeedsCompilation: yes Package: sizepower Version: 1.68.0 Depends: stats License: LGPL MD5sum: 34414b6dda2afcd483187d55a3b37da3 NeedsCompilation: no Package: skewr Version: 1.30.0 Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports: minfi, S4Vectors (>= 0.19.1), RColorBrewer Suggests: GEOquery, knitr, minfiData License: GPL-2 MD5sum: 7f8746c530c03e39121e33b80d8a2ac3 NeedsCompilation: no Package: slalom Version: 1.20.2 Depends: R (>= 4.0) Imports: Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase, methods, rsvd, SingleCellExperiment, SummarizedExperiment, stats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat License: GPL-2 MD5sum: b077d8852c96e7c28ed9b07e8e4ae720 NeedsCompilation: yes Package: slingshot Version: 2.6.0 Depends: R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils Imports: graphics, grDevices, igraph, matrixStats, methods, S4Vectors, SingleCellExperiment, SummarizedExperiment Suggests: BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr License: Artistic-2.0 MD5sum: 25f2470b7f5f3d2e2757391ceebbe33c NeedsCompilation: no Package: SLqPCR Version: 1.64.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) MD5sum: 0462865c03c2248636e5791995b5c260 NeedsCompilation: no Package: SMAD Version: 1.14.1 Depends: R (>= 3.6.0), RcppAlgos Imports: magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: e42457e28fe90d128b8c2ec4c18039d6 NeedsCompilation: yes Package: SMAP Version: 1.62.0 Depends: R (>= 2.10), methods License: GPL-2 MD5sum: 3d4c8cc9d9a9d4774f49997d51d54755 NeedsCompilation: yes Package: SMITE Version: 1.26.0 Depends: R (>= 3.5), GenomicRanges Imports: scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2, reactome.db, KEGGREST, BioNet, goseq, methods, IRanges, igraph, Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 4fc1a31c3f315c45a92bdcfe446b0726 NeedsCompilation: no Package: SNAGEE Version: 1.38.0 Depends: R (>= 2.6.0), SNAGEEdata Suggests: ALL, hgu95av2.db Enhances: parallel License: Artistic-2.0 MD5sum: c443368f611cb4f692541821c80bd722 NeedsCompilation: no Package: snapCGH Version: 1.68.0 Depends: R (>= 3.5.0) Imports: aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma, methods, stats, tilingArray, utils License: GPL MD5sum: 63d0bbd47335c3ea33a5ffa35c714d4a NeedsCompilation: yes Package: snapcount Version: 1.10.0 Depends: R (>= 4.0.0) Imports: R6, httr, rlang, purrr, jsonlite, assertthat, data.table, Matrix, magrittr, methods, stringr, stats, IRanges, GenomicRanges, SummarizedExperiment Suggests: BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 6e35629518385c48604aed59656f4f7c NeedsCompilation: no Package: snifter Version: 1.8.0 Depends: R (>= 4.0.0) Imports: basilisk, reticulate, irlba, stats, assertthat Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) License: GPL-3 MD5sum: ac58acec8a50229fab245c980b225615 NeedsCompilation: no Package: snm Version: 1.46.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL MD5sum: d77ab3eb4ad26badb15d9f252eedc533 NeedsCompilation: no Package: SNPediaR Version: 1.24.0 Depends: R (>= 3.0.0) Imports: RCurl, jsonlite Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: cd36052b558077e018db32954cacc6c5 NeedsCompilation: no Package: SNPhood Version: 1.28.0 Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, data.table, checkmate Imports: DESeq2, cluster, ggplot2, lattice, GenomeInfoDb, BiocParallel, VariantAnnotation, BiocGenerics, IRanges, methods, SummarizedExperiment, RColorBrewer, Biostrings, grDevices, gridExtra, stats, grid, utils, reshape2, scales, S4Vectors Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot License: LGPL (>= 3) MD5sum: e509881d53babc41b25387b234856caa NeedsCompilation: no Package: SNPRelate Version: 1.32.2 Depends: R (>= 2.15), gdsfmt (>= 1.8.3) Imports: methods LinkingTo: gdsfmt Suggests: parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics Enhances: SeqArray (>= 1.12.0) License: GPL-3 MD5sum: a8f9659c450f726aa3202848a75fde20 NeedsCompilation: yes Package: snpStats Version: 1.48.0 Depends: R(>= 2.10.0), survival, Matrix, methods Imports: graphics, grDevices, stats, utils, BiocGenerics, zlibbioc Suggests: hexbin License: GPL-3 MD5sum: 73b24be9fc4858866ce533be746f9cfb NeedsCompilation: yes Package: soGGi Version: 1.30.0 Depends: R (>= 3.5.0), BiocGenerics, SummarizedExperiment Imports: methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, preprocessCore, chipseq, BiocParallel Suggests: testthat, BiocStyle, knitr License: GPL (>= 3) MD5sum: 0a34a23bf90610c60d93d9c3de6603b5 NeedsCompilation: no Package: sojourner Version: 1.11.0 Imports: ggplot2,dplyr,reshape2,gridExtra,EBImage,MASS,R.matlab,Rcpp,fitdistrplus,mclust,minpack.lm,mixtools,mltools,nls2,plyr,sampSurf,scales,shiny,shinyjs,sp,truncnorm,utils,stats,pixmap,rlang,graphics,grDevices,grid,compiler,lattice Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: da7adae9490fe1f96134e5e9ec7b2d2c NeedsCompilation: no Package: SomaticSignatures Version: 2.34.0 Depends: R (>= 3.5.0), VariantAnnotation, GenomicRanges, NMF Imports: S4Vectors, IRanges, GenomeInfoDb, Biostrings, ggplot2, ggbio, reshape2, NMF, pcaMethods, Biobase, methods, proxy Suggests: testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva License: MIT + file LICENSE MD5sum: be0b8997e550142d735f842579df68ae NeedsCompilation: no Package: SOMNiBUS Version: 1.6.0 Depends: R (>= 4.1.0) Imports: graphics, Matrix, mgcv, stats, VGAM Suggests: BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 9505cdd8f44ac8d62053d133f354494d NeedsCompilation: no Package: SpacePAC Version: 1.36.0 Depends: R(>= 2.15),iPAC Suggests: RUnit, BiocGenerics, rgl License: GPL-2 MD5sum: 763f06a3c11b0d56aa23ea99d89f1c1d NeedsCompilation: no Package: Spaniel Version: 1.12.0 Depends: R (>= 4.0) Imports: Seurat, SingleCellExperiment, SummarizedExperiment, dplyr, methods, ggplot2, scater (>= 1.13), scran, igraph, shiny, jpeg, magrittr, utils, S4Vectors, DropletUtils, jsonlite, png Suggests: knitr, rmarkdown, testthat, devtools License: MIT + file LICENSE MD5sum: 9ba550a71f017f8fb6f9b51b6bb0ba81 NeedsCompilation: no Package: sparrow Version: 1.4.0 Depends: R (>= 4.0) Imports: babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet, checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>= 1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>= 2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix, methods, plotly (>= 4.9.0), stats, utils, viridis Suggests: AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr, PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot License: MIT + file LICENSE MD5sum: 4a5c45a2864f4460e3731f526ac08473 NeedsCompilation: no Package: sparseDOSSA Version: 1.22.0 Imports: stats, utils, optparse, MASS, tmvtnorm (>= 1.4.10), MCMCpack Suggests: knitr, BiocStyle, BiocGenerics, rmarkdown License: MIT + file LICENSE MD5sum: d106c8ac7b406d1ed166188f021ef5eb NeedsCompilation: no Package: sparseMatrixStats Version: 1.10.0 Depends: MatrixGenerics (>= 1.5.3) Imports: Rcpp, Matrix, matrixStats (>= 0.60.0), methods LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 75d3bc14cc6c7f2d0759c29cbeda81a0 NeedsCompilation: yes Package: sparsenetgls Version: 1.16.0 Depends: R (>= 4.0.0), Matrix, MASS Imports: methods, glmnet, huge, stats, graphics, utils Suggests: testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) License: GPL-3 MD5sum: 8a8efdc7f9153611d00ac70b684bc259 NeedsCompilation: no Package: SparseSignatures Version: 2.8.0 Depends: R (>= 4.1.0), NMF Imports: nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2, gridExtra, reshape2 Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr, License: file LICENSE MD5sum: 42a681efcc2193532d1251874043252b NeedsCompilation: no Package: spaSim Version: 1.0.2 Depends: R (>= 4.2.0) Imports: ggplot2, methods, stats, dplyr, spatstat.geom, spatstat.random, SpatialExperiment, SummarizedExperiment, RANN Suggests: RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown License: Artistic-2.0 MD5sum: 95c108aa17d92ed93e971d1d0dab9528 NeedsCompilation: no Package: SpatialCPie Version: 1.14.0 Depends: R (>= 3.6) Imports: colorspace (>= 1.3-2), data.table (>= 1.12.2), digest (>= 0.6.21), dplyr (>= 0.7.6), ggforce (>= 0.3.0), ggiraph (>= 0.5.0), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), grid (>= 3.5.1), igraph (>= 1.2.2), lpSolve (>= 5.6.13), methods (>= 3.5.0), purrr (>= 0.2.5), readr (>= 1.1.1), rlang (>= 0.2.2), shiny (>= 1.1.0), shinycssloaders (>= 0.2.0), shinyjs (>= 1.0), shinyWidgets (>= 0.4.8), stats (>= 3.6.0), SummarizedExperiment (>= 1.10.1), tibble (>= 1.4.2), tidyr (>= 0.8.1), tidyselect (>= 0.2.4), tools (>= 3.6.0), utils (>= 3.5.0), zeallot (>= 0.1.0) Suggests: BiocStyle (>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0) License: MIT + file LICENSE MD5sum: 9940e07ceb443a0bf4c24d0eb0e24496 NeedsCompilation: no Package: spatialDE Version: 1.4.3 Depends: R (>= 4.1) Imports: reticulate, basilisk (>= 1.9.10), checkmate, stats, SpatialExperiment, methods, SummarizedExperiment, Matrix, S4Vectors, ggplot2, ggrepel, scales, gridExtra Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 8a1e6dff7225af0882157e80d7768c1b NeedsCompilation: no Package: SpatialDecon Version: 1.8.0 Depends: R (>= 4.0.0) Imports: grDevices, stats, utils, graphics, SeuratObject, Biobase, GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4) Suggests: testthat, knitr, rmarkdown, qpdf License: MIT + file LICENSE MD5sum: 32548789c532014650a765197400da79 NeedsCompilation: no Package: SpatialExperiment Version: 1.8.1 Depends: methods, SingleCellExperiment Imports: rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, DropletUtils, BiocGenerics, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix License: GPL-3 MD5sum: 346f3c5815f270e0a50ae487eda2cf21 NeedsCompilation: no Package: SpatialFeatureExperiment Version: 1.0.3 Depends: R (>= 4.2.0) Imports: BiocGenerics, BiocParallel, methods, rjson, S4Vectors, sf, SingleCellExperiment, SpatialExperiment, spdep (>= 1.1-7), SummarizedExperiment, stats, utils Suggests: BiocStyle, DropletUtils, knitr, Matrix, rmarkdown, SFEData, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: ac890508d2b42d035ea46cb68d26171b NeedsCompilation: no Package: spatialHeatmap Version: 2.4.0 Depends: R (>= 3.5.0) Imports: BiocParallel, BiocFileCache, data.table, dplyr, edgeR, WGCNA, flashClust, htmlwidgets, genefilter, ggplot2, ggdendro, grImport, grid, gridExtra, gplots, igraph, limma, methods, Matrix, rsvg, shiny, dynamicTreeCut, grDevices, graphics, ggplotify, parallel, plotly, rappdirs, reshape2, scater, scuttle, scran, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, tibble, utils, visNetwork, UpSetR, xml2, yaml Suggests: av, knitr, rmarkdown, BiocStyle, BiocSingular, RUnit, BiocGenerics, DESeq2, distinct, HDF5Array, kableExtra, magick, ExpressionAtlas, DT, Biobase, GEOquery, pROC, rols, shinyWidgets, shinyjs, htmltools, shinyBS, sortable License: Artistic-2.0 MD5sum: 97791b1e1fa26cb460b988f1dfd1d9e2 NeedsCompilation: no Package: spatzie Version: 1.4.0 Depends: R (>= 4.1) Imports: BiocGenerics, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicInteractions, GenomicRanges, ggplot2, IRanges, matrixStats, motifmatchr, S4Vectors, stats, SummarizedExperiment, TFBSTools, utils Suggests: BiocManager, Biostrings, knitr, pheatmap, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-3 MD5sum: 8332b628b7f696c5fd500736d1053eec NeedsCompilation: no Package: specL Version: 1.32.1 Depends: R (>= 3.6), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.5), RSQLite (>= 1.1), seqinr (>= 3.3) Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) License: GPL-3 MD5sum: e48e023dc22b05f77685e44f49b73519 NeedsCompilation: no Package: SpeCond Version: 1.52.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) MD5sum: c1ce36dd2bb0e01e8944edf1c780d8b8 NeedsCompilation: no Package: Spectra Version: 1.8.3 Depends: R (>= 4.0.0), S4Vectors, BiocParallel, ProtGenerics (>= 1.29.1) Imports: methods, IRanges, MsCoreUtils (>= 1.7.5), graphics, grDevices, stats, tools, utils, fs, BiocGenerics Suggests: testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0) License: Artistic-2.0 MD5sum: 3d3899e739014a2bc40b5503ac8db803 NeedsCompilation: no Package: SpectralTAD Version: 1.14.1 Depends: R (>= 3.6) Imports: dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges, utils Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr License: MIT + file LICENSE MD5sum: f2c8c93d8f1703cfc1ddff92f6a89031 NeedsCompilation: no Package: SPEM Version: 1.38.0 Depends: R (>= 2.15.1), Rsolnp, Biobase, methods License: GPL-2 MD5sum: 1018dfbcf32a28dd000ba36eb4a7d86d NeedsCompilation: no Package: SPIA Version: 2.50.0 Depends: R (>= 2.14.0), graphics, KEGGgraph Imports: graphics Suggests: graph, Rgraphviz, hgu133plus2.db License: file LICENSE License_restricts_use: yes MD5sum: 0ee81ea8f562f47e4272289f3c24e83e NeedsCompilation: no Package: SPIAT Version: 1.0.4 Depends: R (>= 4.2.0), SpatialExperiment Imports: apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3), gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3), plotly (>= 4.9.0), RANN (>= 2.6.1), pracma (>= 2.2.5), dbscan (>= 1.1-5), mmand (>= 1.5.4), tibble (>= 2.1.3), grDevices, stats, utils, vroom, ComplexHeatmap, dittoSeq, spatstat.geom, alphahull, methods, spatstat.explore, raster, sp, elsa, Rtsne, umap, rlang, graphics, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, pkgdown, testthat, xROI License: Artistic-2.0 MD5sum: b21a2edf97f0d59f621da0936717fa99 NeedsCompilation: no Package: spicyR Version: 1.10.7 Depends: R (>= 4.1) Imports: ggplot2, concaveman, BiocParallel, spatstat.explore, spatstat.geom, lmerTest, BiocGenerics, S4Vectors, lme4, methods, mgcv, pheatmap, rlang, grDevices, IRanges, stats, data.table, dplyr, tidyr, scam, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, ggforce Suggests: BiocStyle, knitr, rmarkdown, pkgdown License: GPL (>= 2) MD5sum: 627a4bd11131ac6a0793477e7ce3f631 NeedsCompilation: no Package: SpidermiR Version: 1.28.0 Depends: R (>= 3.0.0) Imports: httr, igraph, utils, stats, miRNAtap, miRNAtap.db, AnnotationDbi, org.Hs.eg.db, gdata Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2 License: GPL (>= 3) MD5sum: 57a99377453421e3cef1cb0603c372aa NeedsCompilation: no Package: spikeLI Version: 2.58.0 Imports: graphics, grDevices, stats, utils License: GPL-2 MD5sum: e40f4f6a6df77dbdddfd08d63201a2bc NeedsCompilation: no Package: spiky Version: 1.4.0 Depends: Rsamtools, GenomicRanges, R (>= 3.6.0) Imports: stats, scales, bamlss, methods, tools, IRanges, Biostrings, GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome, S4Vectors, graphics, ggplot2, utils Suggests: covr, testthat, equatiomatic, universalmotif, kebabs, ComplexHeatmap, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager License: GPL-2 MD5sum: ba3890bcf94f5bf21007ec0c31b98689 NeedsCompilation: no Package: spkTools Version: 1.54.0 Depends: R (>= 2.7.0), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), graphics, grDevices, gtools, methods, RColorBrewer, stats, utils Suggests: xtable License: GPL (>= 2) MD5sum: 9947bbd0341cddb329e7575fe6d2c30d NeedsCompilation: no Package: splatter Version: 1.22.1 Depends: R (>= 4.0), SingleCellExperiment Imports: BiocGenerics, BiocParallel, checkmate (>= 2.0.0), edgeR, fitdistrplus, ggplot2, locfit, matrixStats, methods, scales, scater (>= 1.15.16), stats, SummarizedExperiment, utils, crayon, S4Vectors, grDevices Suggests: BiocStyle, covr, cowplot, magick, knitr, limSolve, lme4, progress, pscl, testthat, preprocessCore, rmarkdown, scDD, scran, mfa, phenopath, BASiCS (>= 1.7.10), zinbwave, SparseDC, BiocManager, spelling, igraph, scuttle, BiocSingular, VariantAnnotation, Biostrings, GenomeInfoDb, GenomicRanges, IRanges License: GPL-3 + file LICENSE MD5sum: dc5ba004d4cec876abaa0d3144716117 NeedsCompilation: no Package: SpliceWiz Version: 1.0.4 Depends: R (>= 3.5.0), NxtIRFdata Imports: ompBAM, methods, stats, utils, tools, parallel, magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2, AnnotationHub, BiocFileCache, BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray, DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges, HDF5Array, IRanges, progress, plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment, S4Vectors, shiny, shinyFiles, shinyWidgets, shinydashboard, rhandsontable, DT, grDevices, heatmaply, pheatmap, matrixStats, RColorBrewer, XML LinkingTo: ompBAM, Rcpp, zlibbioc, RcppProgress Suggests: knitr, rmarkdown, openssl, crayon, egg, DESeq2, limma, DoubleExpSeq, satuRn, edgeR, Rsubread, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 4947ed9baebf2d3a2d62d76d9b01d33a NeedsCompilation: yes Package: SplicingFactory Version: 1.6.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, methods, stats Suggests: testthat, knitr, rmarkdown, ggplot2, tidyr License: GPL-3 + file LICENSE MD5sum: 1fcef6a888994540d411327c992c8a8d NeedsCompilation: no Package: SplicingGraphs Version: 1.38.0 Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22), Rgraphviz (>= 2.3.7) Imports: methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>= 0.17.5), BiocParallel, IRanges (>= 2.21.2), GenomeInfoDb, GenomicRanges (>= 1.23.21), GenomicFeatures, Rsamtools, GenomicAlignments, graph, Rgraphviz Suggests: igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit License: Artistic-2.0 MD5sum: 0ea878203cd5d6433eae5c0275ddea24 NeedsCompilation: no Package: splineTimeR Version: 1.26.0 Depends: R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines, GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs Suggests: knitr License: GPL-3 MD5sum: e053a60bd52bf3218c86b1ffed66d988 NeedsCompilation: no Package: SPLINTER Version: 1.24.0 Depends: R (>= 3.6.0), grDevices, stats Imports: graphics, ggplot2, seqLogo, Biostrings, biomaRt, GenomicAlignments, GenomicRanges, GenomicFeatures, Gviz, IRanges, S4Vectors, GenomeInfoDb, utils, plyr,stringr, methods, BSgenome.Mmusculus.UCSC.mm9, googleVis Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: fd96ab3b07c650f9f62e90e0cf040dda NeedsCompilation: no Package: splots Version: 1.64.0 Imports: grid, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI License: LGPL MD5sum: 04b3fba3517a9ff463b8c3e0eca2a18e NeedsCompilation: no Package: SPONGE Version: 1.20.0 Depends: R (>= 3.6) Imports: Biobase, stats, ppcor, logging, foreach, doRNG, data.table, MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse, caret, dplyr, biomaRt, randomForest, ggridges, cvms, miRBaseConverter, ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr, stringr, tidyr Suggests: testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, digest, doParallel, bigmemory License: GPL (>= 3) MD5sum: f178a02957a183a3b3ca0b03cab8d269 NeedsCompilation: no Package: SpotClean Version: 1.0.1 Depends: R (>= 4.2.0), Imports: stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment, SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap, rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling License: GPL-3 MD5sum: ef994e8df5e2584c6418e99f7fd8c023 NeedsCompilation: yes Package: SPOTlight Version: 1.2.0 Depends: R (>= 4.1) Imports: ggplot2, NMF, Matrix, matrixStats, nnls, SingleCellExperiment, stats Suggests: BiocStyle, colorBlindness, ExperimentHub, DelayedArray, ggcorrplot, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, Seurat, SeuratObject, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat License: GPL-3 MD5sum: 558ff8d0c3f5413b6d1ec38e556de0d1 NeedsCompilation: no Package: spqn Version: 1.10.0 Depends: R (>= 4.0), ggplot2, ggridges, SummarizedExperiment, BiocGenerics Imports: graphics, stats, utils, matrixStats Suggests: BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3), RUnit License: Artistic-2.0 MD5sum: a8acde152f9706f490760735727e1633 NeedsCompilation: no Package: SPsimSeq Version: 1.8.0 Depends: R (>= 4.0) Imports: stats, methods, SingleCellExperiment, fitdistrplus, graphics, edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils Suggests: knitr, rmarkdown, LSD, testthat, BiocStyle License: GPL-2 MD5sum: 1c2cdeaa0b16602ff882f7d8c05c7011 NeedsCompilation: no Package: SQLDataFrame Version: 1.12.0 Depends: R (>= 3.6), dplyr (>= 0.8.0.1), dbplyr (>= 1.4.0), S4Vectors (>= 0.33.3), Imports: DBI, lazyeval, methods, tools, stats, BiocGenerics, RSQLite, tibble Suggests: RMySQL, bigrquery, testthat, knitr, rmarkdown, DelayedArray License: GPL-3 MD5sum: f5f9e191ee962da9f8ac38f890fcc6c1 NeedsCompilation: no Package: SQUADD Version: 1.48.0 Depends: R (>= 2.11.0) Imports: graphics, grDevices, methods, RColorBrewer, stats, utils License: GPL (>= 2) MD5sum: 3f0067adb17f580c8b30ec01eba997df NeedsCompilation: no Package: sRACIPE Version: 1.14.0 Depends: R (>= 3.6.0),SummarizedExperiment, methods, Rcpp Imports: ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork, gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices, stats, utils, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown, tinytest, doFuture License: MIT + file LICENSE MD5sum: d41ea26e3cea7b9f62acb072bf16305e NeedsCompilation: yes Package: SRAdb Version: 1.60.0 Depends: RSQLite, graph, RCurl Imports: GEOquery Suggests: Rgraphviz License: Artistic-2.0 MD5sum: d3d4bf938492669f0d87a5e7a70dc2a2 NeedsCompilation: no Package: srnadiff Version: 1.18.2 Depends: R (>= 3.6) Imports: Rcpp (>= 0.12.8), methods, devtools, S4Vectors, GenomeInfoDb, rtracklayer, SummarizedExperiment, IRanges, GenomicRanges, DESeq2, edgeR, baySeq, Rsamtools, GenomicFeatures, GenomicAlignments, grDevices, Gviz, BiocParallel, BiocStyle, BiocManager LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocManager, BiocStyle License: GPL-3 MD5sum: 7bc319eb88de3845ec9800e7b30af535 NeedsCompilation: yes Package: sscore Version: 1.70.0 Depends: R (>= 1.8.0), affy, affyio Suggests: affydata License: GPL (>= 2) MD5sum: 646d13aa1c3bfad1f1a9932368b908ba NeedsCompilation: no Package: sscu Version: 2.28.0 Depends: R (>= 3.3) Imports: Biostrings (>= 2.36.4), seqinr (>= 3.1-3), BiocGenerics (>= 0.16.1) Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 61ae5fc803ed23477985344353be6f6e NeedsCompilation: no Package: sSeq Version: 1.36.0 Depends: R (>= 3.0), caTools, RColorBrewer License: GPL (>= 3) MD5sum: 61d94e7af49cfcfa75b16febc9ecb0e6 NeedsCompilation: no Package: ssize Version: 1.72.0 Depends: gdata, xtable License: LGPL MD5sum: 9168306f7c0b233a935f340e7086ee0b NeedsCompilation: no Package: sSNAPPY Version: 1.2.5 Depends: R (>= 4.2.0) Imports: dplyr, magrittr, rlang, stats, purrr, BiocParallel, graphite, Rcpp, tibble, ggplot2, ggraph, igraph, reshape2, org.Hs.eg.db, SummarizedExperiment, edgeR, methods, ggforce, ggnewscale, pheatmap, utils LinkingTo: Rcpp, RcppArmadillo Suggests: BiocManager, BiocStyle, cowplot, DT, htmltools, knitr, pander, rmarkdown, spelling, stringr, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: b858c629a43f0926eebe655fcdba2cc3 NeedsCompilation: yes Package: ssPATHS Version: 1.12.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: ROCR, dml, MESS Suggests: ggplot2, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: f791c02bf518ea43493ec9028761b680 NeedsCompilation: no Package: ssrch Version: 1.14.0 Depends: R (>= 3.6), methods Imports: shiny, DT, utils Suggests: knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: 5d17c0e4261e24df2d4ddc9a8900c972 NeedsCompilation: no Package: ssviz Version: 1.32.0 Depends: R (>= 3.5.0), methods, Rsamtools, Biostrings, reshape, ggplot2, RColorBrewer, stats Suggests: knitr License: GPL-2 MD5sum: cd6def90c1942acb00bb22ba471a14c1 NeedsCompilation: no Package: stageR Version: 1.20.0 Depends: R (>= 3.4), SummarizedExperiment Imports: methods, stats Suggests: knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma, DEXSeq, testthat License: GNU General Public License version 3 MD5sum: d4903f948fd25eb67e2fc0e672a7bb13 NeedsCompilation: no Package: STAN Version: 2.26.2 Depends: R (>= 3.5.0), methods, poilog, parallel Imports: GenomicRanges, IRanges, S4Vectors, BiocGenerics, GenomeInfoDb, Gviz, Rsolnp Suggests: BiocStyle, gplots, knitr License: GPL (>= 2) MD5sum: 89d239aa5a28eefddf036067bb2700f9 NeedsCompilation: yes Package: standR Version: 1.2.2 Depends: R (>= 4.1) Imports: dplyr, SpatialExperiment (>= 1.5.2), SummarizedExperiment, SingleCellExperiment, edgeR, rlang, readr, tibble, ggplot2, tidyr, ruv, limma, patchwork, S4Vectors, Biobase, BiocGenerics, grDevices, stats, methods, ggalluvial, mclustcomp, RUVSeq Suggests: knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 8abb663bb8b29df08f1907c54bf21fb7 NeedsCompilation: no Package: staRank Version: 1.40.0 Depends: methods, cellHTS2, R (>= 2.10) License: GPL MD5sum: ddd351fb50d195137855f1f956593930 NeedsCompilation: no Package: StarBioTrek Version: 1.24.0 Depends: R (>= 3.3) Imports: SpidermiR, graphite, AnnotationDbi, e1071, ROCR, MLmetrics, grDevices, igraph, reshape2, ggplot2 Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, qgraph, png, grid License: GPL (>= 3) MD5sum: 4fdfb4f3a0e48b0196d748b51250779a NeedsCompilation: no Package: STATegRa Version: 1.34.0 Depends: R (>= 2.10) Imports: Biobase, gridExtra, ggplot2, methods, stats, grid, MASS, calibrate, gplots, edgeR, limma, foreach, affy Suggests: RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>= 1.3), roxygen2, doSNOW License: GPL-2 MD5sum: f27300e8dd916357a779d4dda4fba2d5 NeedsCompilation: no Package: Statial Version: 1.0.1 Depends: R (>= 4.1.0) Imports: BiocParallel, spatstat.geom, concaveman, tidyverse, data.table, spatstat.explore, dplyr, tidyr, SingleCellExperiment, tibble, stringr, tidyselect, ggplot2, methods, stats Suggests: BiocStyle, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: a14af7908d2777f9af41347b79f513e6 NeedsCompilation: no Package: statTarget Version: 1.28.0 Depends: R (>= 3.6.0) Imports: randomForest,plyr,pdist,ROC,utils,grDevices,graphics,rrcov,stats, pls,impute Suggests: testthat, BiocStyle, knitr, rmarkdown License: LGPL (>= 3) MD5sum: 038dad1d3a88ec499eadec71c487fd31 NeedsCompilation: no Package: STdeconvolve Version: 1.2.0 Depends: R (>= 4.1) Imports: topicmodels, BiocParallel, Matrix, methods, mgcv, ggplot2, scatterpie, viridis, slam, stats, clue, liger, reshape2, graphics, grDevices, utils Suggests: knitr, BiocStyle, rmarkdown, testthat, rcmdcheck, gplots, gridExtra, hash, dplyr, parallel License: GPL-3 MD5sum: 1702064f1c73e0e9edcfa3d6fed9f95f NeedsCompilation: no Package: stepNorm Version: 1.70.0 Depends: R (>= 1.8.0), marray, methods Imports: marray, MASS, methods, stats License: LGPL MD5sum: db5dae4267cc0357e7ec70262746ceb8 NeedsCompilation: no Package: stJoincount Version: 1.0.0 Depends: R (>= 4.2.0) Imports: graphics, stats, dplyr, magrittr, sp, raster, spdep, ggplot2, pheatmap, grDevices, Seurat, SpatialExperiment, SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 74904917e330f82631376e7327aa2ff5 NeedsCompilation: no Package: strandCheckR Version: 1.16.0 Imports: dplyr, magrittr, GenomeInfoDb, GenomicAlignments, GenomicRanges, IRanges, Rsamtools, S4Vectors, grid, BiocGenerics, ggplot2, reshape2, stats, gridExtra, TxDb.Hsapiens.UCSC.hg38.knownGene, methods, stringr, rmarkdown Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 569154fa79aead9bfc49e48fd1f747ca NeedsCompilation: no Package: Streamer Version: 1.44.0 Imports: methods, graph, RBGL, parallel, BiocGenerics Suggests: RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz License: Artistic-2.0 MD5sum: 3243c67591846bfea9fd0bea5f241a08 NeedsCompilation: yes Package: STRINGdb Version: 2.10.1 Depends: R (>= 2.14.0) Imports: png, sqldf, plyr, igraph, RCurl, methods, RColorBrewer, gplots, hash, plotrix Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: ba51dc879a5187d02406748a16b9e5d1 NeedsCompilation: no Package: STROMA4 Version: 1.22.0 Depends: R (>= 3.4), Biobase, BiocParallel, cluster, matrixStats, stats, graphics, utils Suggests: breastCancerMAINZ License: GPL-3 MD5sum: c1b42b9b8c370631df85a136ed4b9b8a NeedsCompilation: no Package: struct Version: 1.10.0 Depends: R (>= 4.0) Imports: methods,ontologyIndex, datasets, graphics, stats, utils, knitr, SummarizedExperiment, S4Vectors, rols Suggests: testthat, rstudioapi, rmarkdown, covr, BiocStyle, openxlsx, ggplot2, magick License: GPL-3 MD5sum: f982aab8ef27607a0be3b14be1407386 NeedsCompilation: no Package: Structstrings Version: 1.14.0 Depends: R (>= 4.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), Biostrings (>= 2.57.2) Imports: methods, BiocGenerics, XVector, stringr, stringi, crayon, grDevices LinkingTo: IRanges, S4Vectors Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle License: Artistic-2.0 MD5sum: 412ce168c7dffa496268217bb8283023 NeedsCompilation: yes Package: structToolbox Version: 1.10.1 Depends: R (>= 4.0), struct (>= 1.5.1) Imports: ggplot2, ggthemes, grid, gridExtra, methods, scales, sp, stats, utils Suggests: agricolae, BiocFileCache, BiocStyle, car, covr, cowplot, e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls, pmp, reshape2, ropls, rmarkdown, Rtsne, testthat, rappdirs License: GPL-3 MD5sum: 972d651172f9c6270442c95a4ac7ee86 NeedsCompilation: no Package: StructuralVariantAnnotation Version: 1.14.1 Depends: GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 4.1.0) Imports: assertthat, Biostrings, stringr, dplyr, methods, rlang, GenomicFeatures, IRanges, S4Vectors, SummarizedExperiment, GenomeInfoDb, Suggests: ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown, tidyverse, knitr, ggbio, biovizBase, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, License: GPL-3 + file LICENSE MD5sum: 4a30636d95f897549092112967511793 NeedsCompilation: no Package: SubCellBarCode Version: 1.14.0 Depends: R (>= 3.6) Imports: Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra, networkD3, ggrepel, graphics, stats, org.Hs.eg.db, AnnotationDbi Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 1947da90b7589005e078ec89423052fb NeedsCompilation: no Package: subSeq Version: 1.28.0 Depends: R (>= 3.2) Imports: data.table, dplyr, tidyr, ggplot2, magrittr, qvalue (>= 1.99), digest, Biobase Suggests: limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr License: MIT + file LICENSE MD5sum: 3271ea6acdf8a4370f9fd68a47c72039 NeedsCompilation: no Package: SUITOR Version: 1.0.0 Depends: R (>= 4.2.0) Imports: stats, utils, graphics, ggplot2, BiocParallel Suggests: devtools, MutationalPatterns, RUnit, BiocManager, BiocGenerics, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 8d4ec4d05c6239e4b7c3fb66a7616264 NeedsCompilation: yes Package: SummarizedBenchmark Version: 2.16.0 Depends: R (>= 3.6), tidyr, SummarizedExperiment, S4Vectors, BiocGenerics, methods, UpSetR, rlang, stringr, utils, BiocParallel, ggplot2, mclust, dplyr, digest, sessioninfo, crayon, tibble Suggests: iCOBRA, BiocStyle, rmarkdown, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt License: GPL (>= 3) MD5sum: decc3374f1f4a63a844bf0ea667898e0 NeedsCompilation: no Package: SummarizedExperiment Version: 1.28.0 Depends: R (>= 4.0.0), methods, MatrixGenerics (>= 1.1.3), GenomicRanges (>= 1.41.5), Biobase Imports: utils, stats, tools, Matrix, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.33.7), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), DelayedArray (>= 0.15.10) Suggests: HDF5Array (>= 1.7.5), annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, jsonlite, rhdf5, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit, testthat, digest License: Artistic-2.0 MD5sum: ebe83ab2c9515946b79b94ecc9a04c3c NeedsCompilation: no Package: Summix Version: 2.4.0 Depends: R (>= 4.1) Imports: nloptr, methods Suggests: rmarkdown, markdown, knitr License: MIT + file LICENSE MD5sum: bc5f7036a26622c777fdd02b400c2996 NeedsCompilation: no Package: supersigs Version: 1.6.0 Depends: R (>= 4.1) Imports: assertthat, caret, dplyr, tidyr, rsample, methods, rlang, utils, Biostrings, stats, SummarizedExperiment Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, testthat, VariantAnnotation License: GPL-3 MD5sum: 49cfd96235732486d67c5176889685ce NeedsCompilation: no Package: supraHex Version: 1.36.0 Depends: R (>= 3.6), hexbin Imports: ape, MASS, grDevices, graphics, stats, readr, tibble, tidyr, dplyr, stringr, purrr, magrittr, igraph, methods License: GPL-2 MD5sum: 6c220ff4ae16d78ec3b607bc9df620f8 NeedsCompilation: no Package: surfaltr Version: 1.4.0 Depends: R (>= 4.0) Imports: dplyr (>= 1.0.6), biomaRt (>= 2.46.0), protr (>= 1.6-2), seqinr (>= 4.2-5), ggplot2 (>= 3.3.2), utils (>= 2.10.1), stringr (>= 1.4.0), Biostrings (>= 2.58.0),readr (>= 1.4.0), httr (>= 1.4.2), testthat(>= 3.0.0), xml2(>= 1.3.2), msa (>= 1.22.0), methods (>= 4.0.3) Suggests: knitr, rmarkdown, devtools, kableExtra License: MIT + file LICENSE MD5sum: 61b0802b41060b3b51ab1665e00cc70f NeedsCompilation: no Package: survcomp Version: 1.48.0 Depends: survival, prodlim, R (>= 3.4) Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta, stats, graphics Suggests: Hmisc, clinfun, xtable, Biobase, BiocManager License: Artistic-2.0 MD5sum: dd57b9cd18086ae87f150c7032c9fb68 NeedsCompilation: yes Package: survtype Version: 1.14.0 Depends: SummarizedExperiment, pheatmap, survival, survminer, clustvarsel, stats, utils Suggests: maftools, scales, knitr, rmarkdown License: Artistic-2.0 MD5sum: aecb8987bfdc5d67dcf63a180c4674c0 NeedsCompilation: no Package: sva Version: 3.46.0 Depends: R (>= 3.2), mgcv, genefilter, BiocParallel Imports: matrixStats, stats, graphics, utils, limma, edgeR Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat License: Artistic-2.0 MD5sum: 5d69841c0ad44bab0fdc2b5d75ddfaa7 NeedsCompilation: yes Package: svaNUMT Version: 1.4.0 Depends: GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>= 4.0) Imports: assertthat, stringr, dplyr, methods, rlang, GenomeInfoDb, S4Vectors, GenomicFeatures Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown License: GPL-3 + file LICENSE MD5sum: d1e808b533a592484b5cb9de024d8450 NeedsCompilation: no Package: svaRetro Version: 1.4.0 Depends: GenomicRanges, rtracklayer, BiocGenerics, StructuralVariantAnnotation, R (>= 4.0) Imports: VariantAnnotation, assertthat, Biostrings, stringr, dplyr, methods, rlang, GenomicFeatures, GenomeInfoDb, S4Vectors, utils Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges, circlize, tictoc, IRanges, stats, SummarizedExperiment, rmarkdown License: GPL-3 + file LICENSE MD5sum: 84f9594d028a7791d26b7ea62dea96a1 NeedsCompilation: no Package: SWATH2stats Version: 1.28.0 Depends: R(>= 2.10.0) Imports: data.table, reshape2, ggplot2, stats, grDevices, graphics, utils, biomaRt, methods Suggests: testthat, knitr, rmarkdown Enhances: MSstats, PECA, aLFQ License: GPL-3 MD5sum: 652a9e37d37dedd750fb32021152278d NeedsCompilation: no Package: SwathXtend Version: 2.20.0 Depends: e1071, openxlsx, VennDiagram, lattice License: GPL-2 MD5sum: fed95fd0568e907b6bc90a46b34b5c10 NeedsCompilation: no Package: swfdr Version: 1.24.0 Depends: R (>= 3.4) Imports: methods, splines, stats4, stats Suggests: dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2, rmarkdown, testthat License: GPL (>= 3) MD5sum: 35e13193e069155f2623fbc4f11a3d8c NeedsCompilation: no Package: switchBox Version: 1.34.0 Depends: R (>= 2.13.1), pROC, gplots License: GPL-2 MD5sum: f54ba376ab76a386ea1c335c328b34e2 NeedsCompilation: yes Package: switchde Version: 1.24.0 Depends: R (>= 3.4), SingleCellExperiment Imports: SummarizedExperiment, dplyr, ggplot2, methods, stats Suggests: knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr License: GPL (>= 2) MD5sum: fb994bc073c1a68a331aad99d5b76ea2 NeedsCompilation: no Package: synapsis Version: 1.4.0 Depends: R (>= 4.1) Imports: EBImage, stats, utils, graphics Suggests: knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse, BiocStyle License: MIT + file LICENSE MD5sum: fc0dccb7e5fea77f2b64e8ffbae911fe NeedsCompilation: no Package: synapter Version: 2.22.0 Depends: R (>= 3.1.0), methods, MSnbase (>= 2.1.2) Imports: RColorBrewer, lattice, qvalue, multtest, utils, tools, Biobase, Biostrings, cleaver (>= 1.3.3), readr (>= 0.2), rmarkdown (>= 1.0) Suggests: synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle, knitr License: GPL-2 MD5sum: 3d1e3e743df356ad82b3a2a9dc7ecb7a NeedsCompilation: no Package: synergyfinder Version: 3.6.3 Depends: R (>= 4.0.0) Imports: drc (>= 3.0-1), reshape2 (>= 1.4.4), tidyverse (>= 1.3.0), dplyr (>= 1.0.3), tidyr (>= 1.1.2), purrr (>= 0.3.4), furrr (>= 0.2.2), ggplot2 (>= 3.3.3), ggforce (>= 0.3.2), grid (>= 4.0.2), vegan (>= 2.5-7), gstat (>= 2.0-6), sp (>= 1.4-5), methods (>= 4.0.2), SpatialExtremes (>= 2.0-9), ggrepel (>= 0.9.1), kriging (>= 1.1), plotly (>= 4.9.3), stringr (>= 1.4.0), future (>= 1.21.0), mice (>= 3.13.0), lattice (>= 0.20-41), nleqslv (>= 3.3.2), stats (>= 4.0.2), graphics (>= 4.0.2), grDevices (>= 4.0.2), magrittr (>= 2.0.1), pbapply (>= 1.4-3), metR (>= 0.9.1) Suggests: knitr, rmarkdown License: Mozilla Public License 2.0 MD5sum: ac8d447937580430da7f4269f3ed8c39 NeedsCompilation: no Package: SynExtend Version: 1.10.2 Depends: R (>= 4.2.0), DECIPHER (>= 2.24.0) Imports: methods, Biostrings, S4Vectors, IRanges, utils, stats, parallel, graphics, grDevices Suggests: BiocStyle, knitr, igraph, markdown, rmarkdown License: GPL-3 MD5sum: 1c6641df1ea66beda1bd88c733cf4666 NeedsCompilation: yes Package: synlet Version: 1.28.0 Depends: R (>= 3.2.0), ggplot2 Imports: doBy, dplyr, grid, magrittr, RColorBrewer, RankProd, reshape2 Suggests: knitr, testthat, rmarkdown License: GPL-3 MD5sum: cef6bc081e9d5f31339a8228830e5bed NeedsCompilation: no Package: SynMut Version: 1.14.0 Imports: seqinr, methods, Biostrings, stringr, BiocGenerics Suggests: BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc, glue License: GPL-2 MD5sum: d46c4e5655a2d4df45fe3188ae962947 NeedsCompilation: no Package: syntenet Version: 1.0.4 Depends: R (>= 4.2) Imports: Rcpp (>= 1.0.8), GenomicRanges, rlang, Biostrings, rtracklayer, utils, methods, igraph, stats, grDevices, RColorBrewer, pheatmap, ggplot2, ggnetwork, intergraph, networkD3 LinkingTo: Rcpp, testthat Suggests: BiocStyle, ggtree, labdsv, covr, knitr, rmarkdown, testthat (>= 3.0.0), xml2 License: GPL-3 MD5sum: 10a7002eab7ce77f6e18fec12e9f3a86 NeedsCompilation: yes Package: systemPipeR Version: 2.4.0 Depends: Rsamtools (>= 1.31.2), Biostrings, ShortRead (>= 1.37.1), methods Imports: GenomicRanges, SummarizedExperiment, ggplot2, yaml, stringr, magrittr, S4Vectors, crayon, BiocGenerics, htmlwidgets Suggests: BiocStyle, knitr, rmarkdown, systemPipeRdata, GenomicAlignments, grid, dplyr, testthat, rjson, annotate, AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT, rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools, GenomicFeatures (>= 1.31.3), VariantAnnotation (>= 1.25.11) License: Artistic-2.0 MD5sum: cb33df0647b67074761e0df3cc5caee4 NeedsCompilation: no Package: systemPipeShiny Version: 1.8.1 Depends: R (>= 4.0.0), shiny (>= 1.6.0), spsUtil (>= 0.2.2), spsComps (>= 0.3.2), drawer (>= 0.2) Imports: DT, assertthat, bsplus, crayon, dplyr, ggplot2, htmltools, glue, magrittr, methods, plotly, rlang, rstudioapi, shinyAce, shinyFiles, shinyWidgets, shinydashboard, shinydashboardPlus (>= 2.0.0), shinyjqui, shinyjs, shinytoastr, stringr, stats, styler, tibble, utils, vroom (>= 1.3.1), yaml, R6, RSQLite, openssl Suggests: testthat, BiocStyle, knitr, rmarkdown, systemPipeR (>= 2.2.0), systemPipeRdata (>= 2.0.0), rhandsontable, zip, callr, pushbar, fs, readr, R.utils, DESeq2, SummarizedExperiment, glmpca, pheatmap, grid, ape, Rtsne, UpSetR, tidyr, esquisse (>= 1.1.0), cicerone License: GPL (>= 3) MD5sum: ccc4e2e8ec24202683e481fcb851cb24 NeedsCompilation: no Package: systemPipeTools Version: 1.6.0 Imports: DESeq2, GGally, Rtsne, SummarizedExperiment, ape, dplyr, ggplot2, ggrepel, ggtree, glmpca, pheatmap, plotly, tibble, magrittr, DT, stats Suggests: systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocGenerics, Biostrings, methods License: Artistic-2.0 MD5sum: 51a1df70131eff836ee669a1bbf6750c NeedsCompilation: no Package: TADCompare Version: 1.8.0 Depends: R (>= 4.0) Imports: dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2, tidyr, ggpubr, RColorBrewer, reshape2, cowplot Suggests: BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, rGREAT, SpectralTAD License: MIT + file LICENSE MD5sum: 07692165540958508adabd852bee8a77 NeedsCompilation: no Package: tanggle Version: 1.4.0 Depends: R (>= 4.1), ggplot2 (>= 2.2.0), ggtree Imports: ape (>= 5.0), phangorn (>= 2.5), utils, methods Suggests: tinytest, BiocStyle, ggimage, knitr, rmarkdown License: Artistic-2.0 MD5sum: 2480f1b040c62cfd66b0b69ebf31caf5 NeedsCompilation: no Package: TAPseq Version: 1.10.0 Depends: R (>= 4.0.0) Imports: methods, GenomicAlignments, GenomicRanges, IRanges, BiocGenerics, S4Vectors (>= 0.20.1), GenomeInfoDb, BSgenome, GenomicFeatures, Biostrings, dplyr, tidyr, BiocParallel Suggests: testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer, BiocStyle License: MIT + file LICENSE MD5sum: c017fa2efd661038a4cb667c9a5c7ff8 NeedsCompilation: no Package: target Version: 1.12.0 Depends: R (>= 3.6) Imports: BiocGenerics, GenomicRanges, IRanges, matrixStats, methods, stats, graphics, shiny Suggests: testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS, covr License: GPL-3 MD5sum: 8a1125a27214acd5e92bb42b603dbb38 NeedsCompilation: no Package: TargetDecoy Version: 1.4.0 Depends: R (>= 4.1) Imports: ggplot2, ggpubr, methods, miniUI, mzID, mzR, shiny, stats Suggests: BiocStyle, knitr, msdata, sessioninfo, rmarkdown, gridExtra, testthat (>= 3.0.0), covr License: Artistic-2.0 MD5sum: 72e36c275e0e07c3378964a7a4c0fcef NeedsCompilation: no Package: TargetScore Version: 1.36.0 Depends: pracma, Matrix Suggests: TargetScoreData, gplots, Biobase, GEOquery License: GPL-2 MD5sum: e2a10f9f4a48039ad6a819f05975a004 NeedsCompilation: no Package: TargetSearch Version: 2.0.0 Imports: graphics, grDevices, methods, ncdf4, stats, utils, assertthat Suggests: TargetSearchData, BiocStyle, knitr, tinytest License: GPL (>= 2) MD5sum: 8df8c07d6bac6b02c0870c5f71f4756a NeedsCompilation: yes Package: TarSeqQC Version: 1.28.0 Depends: R (>= 3.5.1), methods, GenomicRanges, Rsamtools (>= 1.9.2), ggplot2, plyr, openxlsx Imports: grDevices, stats, utils, S4Vectors, IRanges, BiocGenerics, reshape2, GenomeInfoDb, BiocParallel, Biostrings, cowplot, graphics, GenomicAlignments, Hmisc Suggests: BiocManager, RUnit License: GPL (>= 2) MD5sum: 6e1741858778147023bc2d1abc837c5c NeedsCompilation: no Package: TBSignatureProfiler Version: 1.10.0 Depends: R (>= 4.2.0) Imports: ASSIGN (>= 1.23.1), BiocGenerics, BiocParallel, ComplexHeatmap, DESeq2, DT, edgeR, gdata, ggplot2, GSVA, magrittr, methods, RColorBrewer, reshape2, rlang, ROCit, S4Vectors, singscore, stats, SummarizedExperiment Suggests: BiocStyle, caret, circlize, class, covr, dplyr, e1071, glmnet, HGNChelper, impute, knitr, lintr, MASS, plyr, pROC, randomForest, rmarkdown, shiny, spelling, sva, testthat License: MIT + file LICENSE MD5sum: 4a82cba1b4a800c2cb1b547353dec36d NeedsCompilation: no Package: TCC Version: 1.38.0 Depends: R (>= 3.0), methods, DESeq2, edgeR, baySeq, ROC Suggests: RUnit, BiocGenerics Enhances: snow License: GPL-2 MD5sum: 12a23d4a631d9b030171a6ada2a281aa NeedsCompilation: no Package: TCGAbiolinks Version: 2.25.3 Depends: R (>= 4.0) Imports: downloader (>= 0.4), grDevices, biomaRt, dplyr, graphics, tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite (>= 1.0.0), plyr, knitr, methods, ggplot2, stringr (>= 1.0.0), IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils, SummarizedExperiment (>= 1.4.0), TCGAbiolinksGUI.data (>= 1.15.1), readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1) Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame, AnnotationHub, ExperimentHub, pathview, clusterProfiler, Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid License: GPL (>= 3) MD5sum: 5afde8cc1dc8402969dbb0a8b91b95f1 NeedsCompilation: no Package: TCGAbiolinksGUI Version: 1.23.0 Depends: R (>= 3.3.1), shinydashboard (>= 0.5.3), TCGAbiolinksGUI.data Imports: shiny (>= 0.14.1), downloader (>= 0.4), grid, DT, plotly, readr, maftools, stringr (>= 1.1.0), SummarizedExperiment, ggrepel, data.table, caret, shinyFiles (>= 0.6.2), ggplot2 (>= 2.1.0), pathview, ELMER (>= 2.0.0), clusterProfiler, parallel, TCGAbiolinks (>= 2.5.5), shinyjs (>= 0.7), colourpicker, sesame, shinyBS (>= 0.61) Suggests: testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2, BiocStyle, animation, rmarkdown, pander License: GPL (>= 3) MD5sum: 7f2d0ed9452b1738afbdd71e4d688e0a NeedsCompilation: no Package: TCGAutils Version: 1.18.0 Depends: R (>= 4.2.0) Imports: AnnotationDbi, BiocGenerics, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment (>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2 Suggests: AnnotationHub, BiocFileCache, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 25c4dc4801b06776e510643c1376d7da NeedsCompilation: no Package: TCseq Version: 1.22.6 Depends: R (>= 3.4) Imports: edgeR, BiocGenerics, reshape2, GenomicRanges, IRanges, SummarizedExperiment, GenomicAlignments, Rsamtools, e1071, cluster, ggplot2, grid, grDevices, stats, utils, methods, locfit Suggests: testthat License: GPL (>= 2) MD5sum: 9c30b9dbc0b1bf244bd0b5d3444a7a50 NeedsCompilation: no Package: TDARACNE Version: 1.47.0 Depends: GenKern, Rgraphviz, Biobase License: GPL-2 MD5sum: 81de074a2c2d3b99621259e550c4b48b NeedsCompilation: no Package: TEKRABber Version: 1.2.0 Depends: R (>= 4.1) Imports: apeglm, biomaRt, DESeq2, Rcpp (>= 1.0.7), SCBN, SummarizedExperiment, stats, utils LinkingTo: Rcpp Suggests: BiocStyle, ggpubr, rmarkdown, shiny, knitr, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 16a4253a47f26d2ac6b4fcdf21d4f1fb NeedsCompilation: yes Package: TENxIO Version: 1.0.1 Depends: R (>= 4.2.0), SingleCellExperiment, SummarizedExperiment Imports: BiocBaseUtils, BiocGenerics, BiocIO, GenomeInfoDb, GenomicRanges, Matrix, MatrixGenerics, methods, RCurl, readr, R.utils, S4Vectors, utils Suggests: BiocStyle, DropletTestFiles, ExperimentHub, HDF5Array, knitr, RaggedExperiment, rhdf5, rmarkdown, Rsamtools, tinytest License: Artistic-2.0 MD5sum: 42126bb9a4ca896a9dfc9e19511e9f44 NeedsCompilation: no Package: tenXplore Version: 1.20.0 Depends: R (>= 4.0), shiny, restfulSE (>= 0.99.12) Imports: methods, ontoProc (>= 0.99.7), SummarizedExperiment, AnnotationDbi, matrixStats, org.Mm.eg.db, stats, utils Suggests: org.Hs.eg.db, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 4e1563821ba68558aea2382b37a23ad2 NeedsCompilation: no Package: TEQC Version: 4.20.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Rsamtools, hwriter Imports: Biobase (>= 2.15.1) License: GPL (>= 2) MD5sum: b95b2e99070291633668d7502e461678 NeedsCompilation: no Package: ternarynet Version: 1.42.0 Depends: R (>= 4.0) Imports: utils, igraph, methods, graphics, stats, BiocParallel Suggests: testthat Enhances: Rmpi, snow License: GPL (>= 2) MD5sum: 6f78dc913b97261c00e84e7f98a75978 NeedsCompilation: yes Package: terraTCGAdata Version: 1.2.0 Depends: R (>= 4.2.0), AnVIL, MultiAssayExperiment Imports: BiocFileCache, dplyr, GenomicRanges, methods, RaggedExperiment, readr, S4Vectors, stats, tidyr, TCGAutils, utils Suggests: knitr, rmarkdown, BiocStyle, withr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 3221a03fdf1396b4e2a49c65e6f87416 NeedsCompilation: no Package: TFARM Version: 1.20.0 Depends: R (>= 3.5.0) Imports: arules, fields, GenomicRanges, graphics, stringr, methods, stats, gplots Suggests: BiocStyle, knitr, plyr License: Artistic-2.0 MD5sum: 9e2b009df5b44b3eb068c6d6397b670a NeedsCompilation: no Package: TFBSTools Version: 1.36.0 Depends: R (>= 3.2.2) Imports: Biobase(>= 2.28), Biostrings(>= 2.36.4), BiocGenerics(>= 0.14.0), BiocParallel(>= 1.2.21), BSgenome(>= 1.36.3), caTools(>= 1.17.1), CNEr(>= 1.4.0), DirichletMultinomial(>= 1.10.0), GenomeInfoDb(>= 1.6.1), GenomicRanges(>= 1.20.6), gtools(>= 3.5.0), grid, IRanges(>= 2.2.7), methods, DBI (>= 0.6), RSQLite(>= 1.0.0), rtracklayer(>= 1.28.10), seqLogo(>= 1.34.0), S4Vectors(>= 0.9.25), TFMPvalue(>= 0.0.5), XML(>= 3.98-1.3), XVector(>= 0.8.0), parallel Suggests: BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr(>= 1.11), testthat, JASPAR2016(>= 1.0.0), JASPAR2018(>= 1.0.0), rmarkdown License: GPL-2 MD5sum: f908ba9781df2d61148fc5917705f7db NeedsCompilation: yes Package: TFEA.ChIP Version: 1.18.0 Depends: R (>= 3.5) Imports: GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices, dplyr, stats, utils, R.utils, methods, org.Hs.eg.db Suggests: knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, DESeq2, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 9aa80290e35d064a55ea90ec42cd38a1 NeedsCompilation: no Package: TFHAZ Version: 1.20.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods, ORFik Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 81fe2f7eeb0d80381bd27accfe1ee059 NeedsCompilation: no Package: TFutils Version: 1.18.0 Depends: R (>= 4.1.0) Imports: methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase, rjson, BiocFileCache, DT, httr, readxl, AnnotationDbi, org.Hs.eg.db, utils Suggests: knitr, data.table, testthat, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer, rmarkdown License: Artistic-2.0 MD5sum: 779b08559c6b039c5b422f9cf36a76c6 NeedsCompilation: no Package: tidybulk Version: 1.10.1 Depends: R (>= 4.1.0) Imports: tibble, readr, dplyr, magrittr, tidyr, stringi, stringr, rlang, purrr, tidyselect, preprocessCore, stats, parallel, utils, lifecycle, scales, SummarizedExperiment, GenomicRanges, methods, S4Vectors, crayon Suggests: BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, igraph, EGSEA License: GPL-3 MD5sum: 693e44897fc005741ff72c1f511279dd NeedsCompilation: no Package: tidySingleCellExperiment Version: 1.8.2 Depends: R (>= 4.0.0), ttservice, SingleCellExperiment Imports: SummarizedExperiment, dplyr, tibble, tidyr, ggplot2, plotly, magrittr, rlang, purrr, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, pillar, stringr, cli, fansi Suggests: BiocStyle, testthat, knitr, markdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, Matrix, uwot, celldex, dittoSeq, EnsDb.Hsapiens.v86 License: GPL-3 MD5sum: 72dd21b78d01687f6a9f8e2c95683b97 NeedsCompilation: no Package: tidySummarizedExperiment Version: 1.8.1 Depends: R (>= 4.0.0), SummarizedExperiment Imports: tibble (>= 3.0.4), dplyr, magrittr, tidyr, ggplot2, rlang, purrr, lifecycle, methods, plotly, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi Suggests: BiocStyle, testthat, knitr, markdown License: GPL-3 MD5sum: 7568eace449e2978cea306944440b5b3 NeedsCompilation: no Package: tigre Version: 1.52.0 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, AnnotationDbi, gplots, graphics, grDevices, stats, utils, annotate, DBI, RSQLite Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager License: AGPL-3 MD5sum: 4cf1e1fcc9a8ffe4df11fd396d377ccc NeedsCompilation: yes Package: TileDBArray Version: 1.8.0 Depends: DelayedArray (>= 0.15.16) Imports: methods, Rcpp, tiledb, S4Vectors LinkingTo: Rcpp Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat License: MIT + file LICENSE MD5sum: ce512bce0bcab97cb7dfa89cc6c698d3 NeedsCompilation: yes Package: tilingArray Version: 1.76.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 MD5sum: db497c7a02fc20e9e761363e8d355127 NeedsCompilation: yes Package: timecourse Version: 1.70.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL MD5sum: ef063c2d4a6c4c361c15e067b1002853 NeedsCompilation: no Package: timeOmics Version: 1.10.0 Depends: mixOmics, R (>= 4.0) Imports: dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, propr, lmtest, plyr Suggests: BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots License: GPL-3 MD5sum: 967874e6cc33f8ad51ec8c5f879bf51f NeedsCompilation: no Package: timescape Version: 1.22.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), stringr (>= 1.0.0), dplyr (>= 0.4.3), gtools (>= 3.5.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 26eb09368fda9c2d6e31e94f96379fb7 NeedsCompilation: no Package: TimiRGeN Version: 1.8.0 Depends: R (>= 4.1), Mfuzz, MultiAssayExperiment Imports: biomaRt, clusterProfiler, dplyr (>= 0.8.4), FreqProf, gtools (>= 3.8.1), gplots, ggdendro, gghighlight, ggplot2, graphics, grDevices, igraph (>= 1.2.4.2), RCy3, readxl, reshape2, rWikiPathways, scales, stats, tidyr (>= 1.0.2), stringr (>= 1.4.0) Suggests: BiocManager, kableExtra, knitr (>= 1.27), org.Hs.eg.db, org.Mm.eg.db, testthat, rmarkdown License: GPL-3 MD5sum: 9eb549b65cb9047c272a6c9229404fe8 NeedsCompilation: no Package: TIN Version: 1.30.0 Depends: R (>= 2.12.0), data.table, impute, aroma.affymetrix Imports: WGCNA, squash, stringr Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: d861f54c0fbb411b291242e97c22dfe0 NeedsCompilation: no Package: TissueEnrich Version: 1.18.0 Depends: R (>= 3.5), ensurer (>= 1.1.0), ggplot2 (>= 2.2.1), SummarizedExperiment (>= 1.6.5), GSEABase (>= 1.38.2) Imports: dplyr (>= 0.7.3), tidyr (>= 0.8.0), stats Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 66d1517d81b3a0820ba5f31b7de8897a NeedsCompilation: no Package: TitanCNA Version: 1.36.0 Depends: R (>= 3.5.1) Imports: BiocGenerics (>= 0.31.6), IRanges (>= 2.6.1), GenomicRanges (>= 1.24.3), VariantAnnotation (>= 1.18.7), foreach (>= 1.4.3), GenomeInfoDb (>= 1.8.7), data.table (>= 1.10.4), dplyr (>= 0.5.0), License: GPL-3 MD5sum: 0cd1ed23092554bf772dabd6ecf7f789 NeedsCompilation: yes Package: tkWidgets Version: 1.76.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 MD5sum: c0beebd9f2d5e41045c916781192bb39 NeedsCompilation: no Package: tLOH Version: 1.6.0 Depends: R (>= 4.2) Imports: scales, stats, utils, ggplot2, data.table, purrr, dplyr, VariantAnnotation, GenomicRanges, MatrixGenerics, bestNormalize, depmixS4, naniar, stringr Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 10d4ea1a71e6973a284038f909611192 NeedsCompilation: no Package: TMixClust Version: 1.20.0 Depends: R (>= 3.4) Imports: gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel, flexclust, grDevices, graphics, Biobase, SPEM Suggests: rmarkdown, knitr, BiocStyle, testthat License: GPL (>= 2) MD5sum: 76cb81a8acc87a1b7dd5ee534a309ac6 NeedsCompilation: no Package: TNBC.CMS Version: 1.14.0 Depends: R (>= 3.6.0), e1071, quadprog, SummarizedExperiment Imports: GSVA (>= 1.26.0), pheatmap, grDevices, RColorBrewer, pracma, GGally, R.utils, forestplot, ggplot2, ggpubr, survival, grid, stats, methods Suggests: knitr License: GPL-3 MD5sum: 314b1384a31ac1ccc1d5c9e5b8c4a74e NeedsCompilation: no Package: TnT Version: 1.20.0 Depends: R (>= 3.4), GenomicRanges Imports: methods, stats, utils, grDevices, htmlwidgets, jsonlite, data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr Suggests: GenomicFeatures, shiny, BiocManager, rmarkdown, testthat License: AGPL-3 MD5sum: a658e628d0cd011c9790b5e4a863edd2 NeedsCompilation: no Package: TOAST Version: 1.12.0 Depends: R (>= 3.6), EpiDISH, limma, nnls, quadprog Imports: stats, methods, SummarizedExperiment, corpcor, doParallel, parallel, ggplot2, tidyr, GGally Suggests: BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix License: GPL-2 MD5sum: 19d4a9cfaee4758a218b62b3f39710a3 NeedsCompilation: no Package: tomoda Version: 1.8.0 Depends: R (>= 4.0.0) Imports: methods, stats, grDevices, reshape2, Rtsne, umap, RColorBrewer, ggplot2, ggrepel, SummarizedExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 52a7481bd26fa5e0240d7bf6fff8236b NeedsCompilation: no Package: tomoseqr Version: 1.2.0 Depends: R (>= 4.2) Imports: grDevices, graphics, animation, tibble, dplyr, stringr, purrr, methods, shiny, BiocFileCache, readr, tools, plotly, ggplot2 Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 9b339c66c67d881e3de6c4706ff499eb NeedsCompilation: no Package: topconfects Version: 1.14.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, assertthat, ggplot2 Suggests: limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle License: LGPL-2.1 | file LICENSE MD5sum: 0e5c2485aff039d6f5d39dc4d791d06b NeedsCompilation: no Package: topdownr Version: 1.20.0 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.20.0), ProtGenerics (>= 1.10.0), Biostrings (>= 2.42.1), S4Vectors (>= 0.12.2) Imports: grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2), MSnbase (>= 2.3.10), ggplot2 (>= 2.2.1), mzR (>= 2.27.5) Suggests: topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2 License: GPL (>= 3) MD5sum: a118dd4c6d72d5c7be989e1a7e25bee4 NeedsCompilation: no Package: topGO Version: 2.50.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.6), graph (>= 1.14.0), Biobase (>= 2.0.0), GO.db (>= 2.3.0), AnnotationDbi (>= 1.7.19), SparseM (>= 0.73) Imports: lattice, matrixStats, DBI Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest License: LGPL MD5sum: f9797ef2a4716a4e6f7d2f2c0acbfb69 NeedsCompilation: no Package: ToxicoGx Version: 2.2.0 Depends: R (>= 4.1), CoreGx Imports: SummarizedExperiment, BiocGenerics, S4Vectors, Biobase, BiocParallel, ggplot2, tibble, dplyr, caTools, downloader, magrittr, methods, reshape2, tidyr, data.table, assertthat, scales, graphics, grDevices, parallel, stats, utils, limma, jsonlite Suggests: rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools, PharmacoGx, xtable, markdown License: MIT + file LICENSE MD5sum: c374971908c993adba7e5d9aca528181 NeedsCompilation: no Package: TPP Version: 3.26.1 Depends: R (>= 3.4), Biobase, dplyr, magrittr, tidyr Imports: biobroom, broom, data.table, doParallel, foreach, futile.logger, ggplot2, grDevices, gridExtra, grid, knitr, limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr, purrr, RColorBrewer, RCurl, reshape2, rmarkdown, splines, stats, stringr, tibble, utils, VennDiagram, VGAM Suggests: BiocStyle, testthat License: Artistic-2.0 MD5sum: 14eb8e2ff969efaabde4564d58faaafb NeedsCompilation: no Package: TPP2D Version: 1.14.0 Depends: R (>= 3.6.0), stats, utils, dplyr, methods Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl, parallel, MASS, BiocParallel, limma Suggests: knitr, testthat, rmarkdown License: GPL-3 MD5sum: fbb04dc6285a3032070945a15b08ddb8 NeedsCompilation: no Package: tracktables Version: 1.32.0 Depends: R (>= 3.5.0) Imports: IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base, stringr, RColorBrewer, methods Suggests: knitr, BiocStyle License: GPL (>= 3) MD5sum: 3f955c8f91ed30c263e3c8667247d20c NeedsCompilation: no Package: trackViewer Version: 1.34.0 Depends: R (>= 3.5.0), grDevices, methods, GenomicRanges, grid, Rcpp Imports: GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, plotrix, Rgraphviz, InteractionSet, graph, utils, rhdf5 LinkingTo: Rcpp Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack License: GPL (>= 2) MD5sum: 550412052e73e2bff301e426fd352584 NeedsCompilation: yes Package: tradeSeq Version: 1.12.0 Depends: R (>= 3.6) Imports: mgcv, edgeR, SingleCellExperiment, SummarizedExperiment, slingshot, magrittr, RColorBrewer, BiocParallel, Biobase, pbapply, igraph, ggplot2, princurve, methods, S4Vectors, tibble, Matrix, TrajectoryUtils, viridis, matrixStats, MASS Suggests: knitr, rmarkdown, testthat, covr, clusterExperiment License: MIT + file LICENSE MD5sum: c51d9231c2694ca6129c3940f693bddc NeedsCompilation: no Package: TrajectoryGeometry Version: 1.6.0 Depends: R (>= 4.1) Imports: pracma, rgl, ggplot2, stats, methods Suggests: dplyr, knitr, RColorBrewer, rmarkdown License: MIT + file LICENSE MD5sum: 1a5951a5f19fe7189b4f0e48956284ae NeedsCompilation: no Package: TrajectoryUtils Version: 1.6.0 Depends: SingleCellExperiment Imports: methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: d213bded89a23b02a3da25319644b0c0 NeedsCompilation: no Package: transcriptogramer Version: 1.20.0 Depends: R (>= 3.4), methods Imports: biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: ff728e344e6d72b0403d3232a4bb194c NeedsCompilation: no Package: transcriptR Version: 1.26.0 Depends: R (>= 3.5.0), methods Imports: BiocGenerics, caret, chipseq, e1071, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2, Rsamtools, rtracklayer, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat License: GPL-3 MD5sum: f86193cd8dde354de1a0ec4174a05606 NeedsCompilation: no Package: transformGamPoi Version: 1.4.0 Imports: glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp LinkingTo: Rcpp Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown License: GPL-3 MD5sum: fe8db1f7e6e1c8f386844e71cbc685a8 NeedsCompilation: yes Package: transite Version: 1.16.0 Depends: R (>= 3.5) Imports: BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0), ggseqlogo (>= 0.1), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils LinkingTo: Rcpp (>= 1.0.4.8) Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: d4df2cace9fd17d5781ba2484b1353af NeedsCompilation: yes Package: tRanslatome Version: 1.36.0 Depends: R (>= 2.15.0), methods, limma, sigPathway, anota, DESeq2, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 MD5sum: 379b1b03daeb81ee625abd4b7c7cd0e7 NeedsCompilation: no Package: transomics2cytoscape Version: 1.8.0 Imports: RCy3, KEGGREST, dplyr, purrr, tibble Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 1e3aed736e319cfd99e796fbb91d9f26 NeedsCompilation: no Package: TransView Version: 1.42.0 Depends: methods, GenomicRanges Imports: BiocGenerics, S4Vectors (>= 0.9.25), IRanges, zlibbioc, gplots LinkingTo: Rhtslib (>= 1.99.1) Suggests: RUnit, pasillaBamSubset, BiocManager License: GPL-3 MD5sum: 0854804a6c5ea43ae5f1a51ba39094f3 NeedsCompilation: yes Package: TraRe Version: 1.5.0 Depends: R (>= 4.1) Imports: hash, ggplot2, stats, methods, igraph, utils, glmnet, vbsr, grDevices, gplots, gtools, pvclust, R.utils, dqrng, SummarizedExperiment, BiocParallel, matrixStats Suggests: knitr, rmarkdown, BiocGenerics, RUnit, BiocStyle License: MIT + file LICENSE MD5sum: 6aa97fed2b4a784bdcc92c9d26632a51 NeedsCompilation: no Package: traseR Version: 1.28.0 Depends: R (>= 3.5.0), GenomicRanges, IRanges, BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL MD5sum: aa0f49946d3ea6ac2cdbfccf681c6925 NeedsCompilation: no Package: Travel Version: 1.6.0 Imports: Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, inline, parallel License: GPL-3 MD5sum: da652100a57515f0dbaf7084fb35525e NeedsCompilation: yes Package: traviz Version: 1.4.0 Depends: R (>= 4.0) Imports: ggplot2, viridis, mgcv, SingleCellExperiment, slingshot, princurve, Biobase, methods, RColorBrewer, SummarizedExperiment, grDevices, graphics, rgl Suggests: scater, dplyr, testthat (>= 3.0.0), covr, S4Vectors, rmarkdown, knitr License: MIT + file LICENSE MD5sum: 6e5797164f2dc1529cc6e8724f76247b NeedsCompilation: no Package: TreeAndLeaf Version: 1.10.0 Depends: R(>= 4.0) Imports: RedeR(>= 1.40.4), igraph, ape Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer License: Artistic-2.0 MD5sum: 5c716b5d382c654865933d805b2505c4 NeedsCompilation: no Package: treeio Version: 1.22.0 Depends: R (>= 3.6.0) Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, tibble, tidytree (>= 0.3.9), utils Suggests: Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml, purrr License: Artistic-2.0 MD5sum: b9488ba3eb48293ae06950a9336703b7 NeedsCompilation: no Package: treekoR Version: 1.6.1 Depends: R (>= 4.1) Imports: stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2, hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt, edgeR, lme4, multcomp Suggests: knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0) License: GPL-3 MD5sum: d874ceff6b8e46248616ae4bde1f627a NeedsCompilation: no Package: TreeSummarizedExperiment Version: 2.6.0 Depends: R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18), Biostrings Imports: methods, BiocGenerics, utils, ape, rlang, dplyr, SummarizedExperiment, BiocParallel, IRanges, treeio Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 9e54fe5296c06b1ba6f98c59027f7017 NeedsCompilation: no Package: TREG Version: 1.2.0 Depends: R (>= 4.2), SummarizedExperiment Imports: Matrix, purrr, rafalib Suggests: BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment License: Artistic-2.0 MD5sum: 72bde92193485231bc3a0761bd1ef8b7 NeedsCompilation: no Package: trena Version: 1.20.0 Depends: R (>= 3.5.0), utils, glmnet (>= 2.0.3), MotifDb (>= 1.19.17) Imports: RSQLite, RMySQL, lassopv, randomForest, xgboost, RPostgreSQL, methods, DBI, BSgenome, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, SNPlocs.Hsapiens.dbSNP150.GRCh38, org.Hs.eg.db, Biostrings, GenomicRanges, biomaRt, AnnotationDbi, WGCNA Suggests: RUnit, plyr, knitr, BiocGenerics, rmarkdown, formatR, markdown, BiocParallel, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Athaliana.TAIR.TAIR9 License: GPL-3 MD5sum: eff8c0040b54fdacb6b0b115ad2279c0 NeedsCompilation: no Package: Trendy Version: 1.20.0 Depends: R (>= 3.4) Imports: stats, utils, graphics, grDevices, segmented, gplots, parallel, magrittr, BiocParallel, DT, S4Vectors, SummarizedExperiment, methods, shiny, shinyFiles Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL-3 MD5sum: 0055a39e66c4c429a9be2d80d871dcf9 NeedsCompilation: no Package: TRESS Version: 1.4.0 Depends: R (>= 4.1.0), parallel, S4Vectors Imports: utils, rtracklayer, Matrix, matrixStats, stats, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi Suggests: knitr, rmarkdown,BiocStyle License: GPL-3 + file LICENSE MD5sum: 964a835ee67e6b7b8acafcda613d1acc NeedsCompilation: no Package: tricycle Version: 1.6.0 Depends: R (>= 4.0), SingleCellExperiment Imports: methods, circular, ggplot2, ggnewscale, AnnotationDbi, scater, GenomicRanges, IRanges, S4Vectors, scattermore, dplyr, RColorBrewer, grDevices, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 376bcece7ed1f6bb66cc857fb12e94bc NeedsCompilation: no Package: trigger Version: 1.44.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 MD5sum: fb4bb1d52ccd745baf796f1fd5569590 NeedsCompilation: yes Package: trio Version: 3.36.0 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1) Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 MD5sum: 2c9061c3b2e2a939343128eaa05b4188 NeedsCompilation: no Package: triplex Version: 1.38.0 Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27), XVector (>= 0.11.6), Biostrings (>= 2.39.10) Imports: methods, grid, GenomicRanges LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer License: BSD_2_clause + file LICENSE MD5sum: e67fc4e3ff830520e30bdeba6c306d73 NeedsCompilation: yes Package: tripr Version: 1.4.0 Depends: shiny (>= 1.6.0), shinyBS Imports: shinyjs, shinyFiles, plyr, data.table, DT, stringr, stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr, pryr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices, graphics, stats, utils Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis Enhances: parallel License: MIT + file LICENSE MD5sum: f4bb70ae994279d2b16fe633d3cb1539 NeedsCompilation: no Package: tRNA Version: 1.16.1 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE MD5sum: 2ac5c488cbf2308cab07cf47ebaa5621 NeedsCompilation: no Package: tRNAdbImport Version: 1.16.0 Depends: R (>= 3.5), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, BiocGenerics, stringr, xml2, S4Vectors, methods, httr, IRanges, utils Suggests: knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE MD5sum: bb0f68515995204b16127530bae60894 NeedsCompilation: no Package: tRNAscanImport Version: 1.18.0 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, stringr, BiocGenerics, Biostrings, Structstrings, S4Vectors, IRanges, XVector, GenomeInfoDb, rtracklayer, BSgenome, Rsamtools Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 + file LICENSE MD5sum: 8572d32d3d35e9d8a60400f8846b8721 NeedsCompilation: no Package: TRONCO Version: 2.30.0 Depends: R (>= 4.1.0), Imports: bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways License: GPL-3 MD5sum: 08f09974b84d53c3628f76b13952ebb4 NeedsCompilation: no Package: TSCAN Version: 1.36.0 Depends: SingleCellExperiment, TrajectoryUtils Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, DelayedArray, S4Vectors Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor License: GPL (>= 2) MD5sum: b40f5a58e7db2ee644afe1b9583d4e95 NeedsCompilation: no Package: tscR Version: 1.10.0 Depends: R (>= 4.1.0), dplyr Imports: gridExtra, methods, dtw, class, kmlShape, graphics, cluster, RColorBrewer, grDevices, knitr, rmarkdown, prettydoc, grid, ggplot2, latex2exp, stats, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors Suggests: testthat License: Artistic-2.0 MD5sum: 70de47cf7873dcd92898d8243a8f0e80 NeedsCompilation: yes Package: ttgsea Version: 1.6.3 Depends: keras Imports: tm, text2vec, tokenizers, textstem, stopwords, data.table, purrr, DiagrammeR, stats Suggests: fgsea, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: bd49eb50b6eab67a2882d0260a8afc72 NeedsCompilation: no Package: TTMap Version: 1.20.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 MD5sum: b3d3bcd7fc6822e1f3a854bed8b6f9ad NeedsCompilation: no Package: TurboNorm Version: 1.46.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata License: LGPL MD5sum: 9754fed558476f702dfeb91c3f40b31b NeedsCompilation: yes Package: TVTB Version: 1.24.0 Depends: R (>= 3.4), methods, utils, stats Imports: AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel, Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges (>= 2.21.6), reshape2, Rsamtools, S4Vectors (>= 0.25.14), SummarizedExperiment, VariantAnnotation (>= 1.19.9) Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander License: Artistic-2.0 MD5sum: 2edad8c2e9c3df0b1c1551b4bac79ce1 NeedsCompilation: no Package: tweeDEseq Version: 1.44.0 Depends: R (>= 2.12.0) Imports: MASS, limma, edgeR, parallel, cqn Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) MD5sum: b1cbbdfdc99eac72276bbf48b6129fac NeedsCompilation: yes Package: twilight Version: 1.74.0 Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, grDevices, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) MD5sum: 90b4852f79f1e3fbcd709b1cae4af226 NeedsCompilation: yes Package: twoddpcr Version: 1.22.0 Depends: R (>= 3.4) Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 8d5875d2cf25aaad313964784255c6bb NeedsCompilation: no Package: txcutr Version: 1.4.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, GenomicFeatures, IRanges, GenomicRanges, BiocGenerics, Biostrings, S4Vectors, rtracklayer, BiocParallel, stats, methods, utils Suggests: RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 MD5sum: 0523d546264d21010fc1494c6608cd58 NeedsCompilation: no Package: tximeta Version: 1.16.1 Imports: SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, tools, utils, methods, Matrix Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools License: GPL-2 MD5sum: 30f52ccaf177a4c334bda9032557d04a NeedsCompilation: no Package: tximport Version: 1.26.1 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds License: LGPL (>= 2) MD5sum: 633cf06a9fd236b1ad5518a7a021390d NeedsCompilation: no Package: TypeInfo Version: 1.64.0 Depends: methods Suggests: Biobase License: BSD_2_clause MD5sum: 19d4bcec9c20ca8c83d06ded6de554d8 NeedsCompilation: no Package: UCell Version: 2.2.0 Depends: R(>= 4.2.0) Imports: methods, data.table(>= 1.13.6), Matrix, BiocParallel, BiocNeighbors, SingleCellExperiment, SummarizedExperiment Suggests: Seurat, scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: e3b72a81583fd418415b8a5329585ec5 NeedsCompilation: no Package: Ularcirc Version: 1.16.0 Depends: R (>= 3.4.0) Imports: AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments, Organism.dplyr, plotgardener, R.utils, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, yaml Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: 994e706cef22c67591683a53e01ed2a6 NeedsCompilation: no Package: UMI4Cats Version: 1.8.1 Depends: R (>= 4.0.0), SummarizedExperiment Imports: magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, magrittr, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats, org.Hs.eg.db, annotate, TxDb.Hsapiens.UCSC.hg19.knownGene, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat License: Artistic-2.0 MD5sum: 5571e5d93940170b12edf3555795a437 NeedsCompilation: no Package: uncoverappLib Version: 1.8.1 Imports: markdown, shiny, shinyjs, shinyBS, shinyWidgets,shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx, condformat, stringr, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache,rappdirs, TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils,S4Vectors, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, processx, Rsamtools, GenomicRanges Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: 6b73517138698bd9aebebfa9aacc3015 NeedsCompilation: no Package: UNDO Version: 1.40.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 669423a1fa44919cc5658cd0a061b73b NeedsCompilation: no Package: unifiedWMWqPCR Version: 1.34.0 Depends: methods Imports: BiocGenerics, stats, graphics, HTqPCR License: GPL (>= 2) MD5sum: f211e2cd9f763e8247634b33004c6087 NeedsCompilation: no Package: UniProt.ws Version: 2.38.1 Depends: methods, utils, RSQLite, BiocGenerics (>= 0.13.8) Imports: AnnotationDbi, BiocFileCache, BiocBaseUtils, rjsoncons, jsonlite, httr, httpcache, progress Suggests: RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 7d05e85235c87ea0de642a1b442fe9ba NeedsCompilation: no Package: Uniquorn Version: 2.18.0 Depends: R (>= 3.5) Imports: stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation, data.table Suggests: testthat, knitr, rmarkdown, BiocGenerics License: Artistic-2.0 MD5sum: 29cbe0d26aaa3866d78607bbfc6b6855 NeedsCompilation: no Package: universalmotif Version: 1.16.0 Depends: R (>= 3.5.0) Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid LinkingTo: Rcpp, RcppThread Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio Enhances: PWMEnrich, rGADEM License: GPL-3 MD5sum: 1fb81c1cc2856bddce67a6b201bb3b52 NeedsCompilation: yes Package: updateObject Version: 1.2.0 Depends: R (>= 4.2.0), methods, BiocGenerics, S4Vectors Imports: utils, digest Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: d61a2390c7b3b7aaa5d54edba8131438 NeedsCompilation: no Package: uSORT Version: 1.24.0 Depends: R (>= 3.3.0), tcltk Imports: igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 MD5sum: e550d257329dce99cce8cefffc8790db NeedsCompilation: no Package: VAExprs Version: 1.4.0 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: 871839f6dd13bf7d7a6c2a9e9c4481be NeedsCompilation: no Package: VanillaICE Version: 1.60.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, human610quadv1bCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 MD5sum: 4426b6a80851eb5ae95a4d4913b681e8 NeedsCompilation: yes Package: VarCon Version: 1.6.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 10099480dde371330d458d120cc4ddcf NeedsCompilation: no Package: variancePartition Version: 1.28.9 Depends: R (>= 4.0.0), ggplot2, limma, BiocParallel Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, foreach, doParallel, gplots, RhpcBLASctl, progress, reshape2, remaCor (>= 0.0.11), aod, scales, Rdpack, rlang, lme4 (>= 1.1-10), grDevices, graphics, Biobase, methods, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr License: GPL-2 MD5sum: 16cb387e7335ea5feddc8832de909b0d NeedsCompilation: no Package: VariantAnnotation Version: 1.44.1 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5), Rsamtools (>= 1.99.0) Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.57.2), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome (>= 1.47.3), GenomicFeatures (>= 1.31.3) LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 1.99.3) Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle License: Artistic-2.0 MD5sum: 4e4c9ebd75a47fb5eab735981d9a8e13 NeedsCompilation: yes Package: VariantExperiment Version: 1.12.0 Depends: R (>= 3.6.0), S4Vectors (>= 0.21.24), SummarizedExperiment (>= 1.13.0), GenomicRanges, Imports: GDSArray (>= 1.11.1), DelayedDataFrame (>= 1.6.0), tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray, SeqVarTools, DelayedArray, Biostrings, IRanges Suggests: testthat, knitr, rmarkdown, markdown License: GPL-3 MD5sum: 7e60243f562e405f96d047f7c6b439cb NeedsCompilation: no Package: VariantFiltering Version: 1.34.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.25.1), VariantAnnotation (>= 1.13.29) Imports: utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Biostrings (>= 2.33.11), GenomeInfoDb (>= 1.3.6), GenomicRanges (>= 1.19.13), SummarizedExperiment, GenomicFeatures, Rsamtools (>= 1.17.8), BSgenome, GenomicScores (>= 1.0.0), Gviz, shiny, shinythemes, shinyjs, DT, shinyTree LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 License: Artistic-2.0 MD5sum: 55c850e8503bfc0043f68ccf3f56072a NeedsCompilation: yes Package: VariantTools Version: 1.40.0 Depends: R (>= 3.5.0), S4Vectors (>= 0.17.33), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), VariantAnnotation (>= 1.11.16), methods Imports: Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel, GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7), BiocParallel, GenomeInfoDb, BSgenome, Biobase Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3) License: Artistic-2.0 MD5sum: 5efec062901de7c8c99b1973c2f96234 NeedsCompilation: no Package: VaSP Version: 1.10.0 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 88de32ec8405843ff7a49e58f64a70d4 NeedsCompilation: no Package: vbmp Version: 1.66.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: 07fb72295810b9ae2b9f5ae8ad2148bb NeedsCompilation: no Package: VCFArray Version: 1.14.0 Depends: R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28) Imports: tools, GenomicRanges, VariantAnnotation (>= 1.29.3), GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown License: GPL-3 MD5sum: ac185a1a7e3fd02704d6fb0e2a55a0ea NeedsCompilation: no Package: VDJdive Version: 1.0.0 Depends: R (>= 4.2) Imports: basilisk, BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix, methods, RColorBrewer, reticulate, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: 9db24834afe1f1015c3f201453907523 NeedsCompilation: no Package: VegaMC Version: 3.36.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods License: GPL-2 MD5sum: 3a0cc3e67f2de4bb8fa8bbcd901f5913 NeedsCompilation: yes Package: velociraptor Version: 1.8.0 Depends: SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors, DelayedArray, basilisk, zellkonverter, scuttle, SingleCellExperiment, BiocParallel, BiocSingular Suggests: BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran, scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot, GGally, patchwork, metR License: MIT + file LICENSE MD5sum: 8658f92ea21c3bfdf30d3e51146c132b NeedsCompilation: no Package: veloviz Version: 1.4.0 Depends: R (>= 4.1) Imports: Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 34fea8e5fabb1e0ac1267834fdd5d357 NeedsCompilation: yes Package: VennDetail Version: 1.14.0 Imports: utils, grDevices, stats, methods, dplyr, purrr, tibble, magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger Suggests: knitr, rmarkdown, testthat, markdown License: GPL-2 MD5sum: 34805acc261d083cd0ea4c499810738d NeedsCompilation: no Package: VERSO Version: 1.8.0 Depends: R (>= 4.1.0) Imports: ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 81acd8bbcb8947ae40608ffecdc24540 NeedsCompilation: no Package: vidger Version: 1.18.0 Depends: R (>= 3.5) Imports: Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr, RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, testthat License: GPL-3 | file LICENSE MD5sum: a10b883b26782abcb2fc1a6516cbf09c NeedsCompilation: no Package: viper Version: 1.32.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: a666dce0810919aabec56c795813f179 NeedsCompilation: no Package: ViSEAGO Version: 1.12.0 Depends: R (>= 3.6) Imports: data.table, AnnotationDbi, AnnotationForge, biomaRt, dendextend, DiagrammeR, DT, dynamicTreeCut, fgsea, GOSemSim, ggplot2, GO.db, grDevices, heatmaply, htmlwidgets, igraph, methods, plotly, processx, topGO, RColorBrewer, R.utils, scales, stats, UpSetR, utils Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager License: GPL-3 MD5sum: fd75bb102de3cad17c566ab7cb5adb6e NeedsCompilation: no Package: vissE Version: 1.6.0 Depends: R (>= 4.1) Imports: igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm, ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb, ggrepel, textstem, tidygraph, stats, scales, ggraph Suggests: testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr License: GPL-3 MD5sum: 928d3a574805cb86456f89cfc7d46c9b NeedsCompilation: no Package: Voyager Version: 1.0.10 Depends: R (>= 4.2.0) Imports: BiocParallel, bluster, ggnewscale, ggplot2 (>= 3.4.0), Matrix, methods, patchwork, rlang, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, SpatialFeatureExperiment, spdep, stats, SummarizedExperiment Suggests: BiocSingular, BiocStyle, cowplot, dbscan, ExperimentHub, hexbin, knitr, rmarkdown, scater, scattermore, scran, SFEData, sparseMatrixStats, testthat (>= 3.0.0), vdiffr License: Artistic-2.0 MD5sum: 9e85d0e2a442622a464b3618549d535f NeedsCompilation: no Package: VplotR Version: 1.8.0 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown License: GPL-3 MD5sum: 240a00c615f71e1d632fcabbd94545dc NeedsCompilation: no Package: vsclust Version: 1.0.0 Depends: R (>= 4.2.0) Imports: matrixStats, limma, parallel, shiny, qvalue, grDevices, stats, MultiAssayExperiment, graphics LinkingTo: Rcpp Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, clusterProfiler License: GPL-2 MD5sum: a554079b30509a0df33c6af585d23189 NeedsCompilation: yes Package: vsn Version: 3.66.0 Depends: R (>= 4.0.0), methods, Biobase Imports: affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat License: Artistic-2.0 MD5sum: b33b39a6724d51e90479f474e1d4d22d NeedsCompilation: yes Package: vtpnet Version: 0.38.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: 0d5870c5466fa6dc389417808d058bab NeedsCompilation: no Package: vulcan Version: 1.20.0 Depends: R (>= 4.0), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene, zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit Imports: wordcloud, csaw, gplots, stats, utils, caTools, graphics, DESeq2, Biobase Suggests: vulcandata License: LGPL-3 MD5sum: a47f0db9f3c3a4d7a9335194b498b4bf NeedsCompilation: no Package: waddR Version: 1.12.0 Depends: R (>= 3.6.0) Imports: Rcpp (>= 1.0.1), arm (>= 1.10-1), eva, BiocFileCache, BiocParallel, SingleCellExperiment, parallel, methods, stats LinkingTo: Rcpp, RcppArmadillo, Suggests: knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown, scater License: MIT + file LICENSE MD5sum: dc7d7fe2bdadbfbc09f35577b01b53ce NeedsCompilation: yes Package: wateRmelon Version: 2.4.0 Depends: R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi, lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19, illuminaio Imports: Biobase Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore Enhances: minfi License: GPL-3 MD5sum: 80eea74751dc0e3314c5e5a44224f7be NeedsCompilation: no Package: wavClusteR Version: 2.32.0 Depends: R (>= 3.2), GenomicRanges (>= 1.31.8), Rsamtools Imports: methods, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Biostrings (>= 2.47.6), foreach, GenomicFeatures (>= 1.31.3), ggplot2, Hmisc, mclust, rtracklayer (>= 1.39.7), seqinr, stringr Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 Enhances: doMC License: GPL-2 MD5sum: e6dcd9461e28235f6fb596d78b163824 NeedsCompilation: no Package: weaver Version: 1.64.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 MD5sum: 5212a28f7b5653089a1bb4d42aae5cf4 NeedsCompilation: no Package: webbioc Version: 1.70.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocManager License: GPL (>= 2) MD5sum: a0e27956105e9032cc113005b5bf24a4 NeedsCompilation: no Package: weitrix Version: 1.10.0 Depends: R (>= 3.6), SummarizedExperiment Imports: methods, utils, stats, grDevices, assertthat, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics, limma, topconfects, dplyr, purrr, ggplot2, rlang, scales, reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl Suggests: knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0) License: LGPL-2.1 | file LICENSE MD5sum: ab7da6c21916674514d701df1b6e4cb2 NeedsCompilation: no Package: widgetTools Version: 1.76.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: 2965b9aa8d0d346be30b38a114e263d9 NeedsCompilation: no Package: wiggleplotr Version: 1.22.0 Depends: R (>= 3.6) Imports: dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer, cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter License: Apache License 2.0 MD5sum: 0a62d512339c8535aefee663271a5552 NeedsCompilation: no Package: wpm Version: 1.8.0 Depends: R (>= 4.1.0) Imports: utils, methods, cli, Biobase, SummarizedExperiment, config, golem, shiny, DT, ggplot2, dplyr, rlang, stringr, shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer, logging Suggests: MSnbase, testthat, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 88d7f95109b7eb3a4e92e1c8107bec9d NeedsCompilation: no Package: wppi Version: 1.6.0 Depends: R(>= 4.1) Imports: dplyr, igraph, logger, methods, magrittr, Matrix, OmnipathR(>= 2.99.8), progress, purrr, rlang, RCurl, stats, tibble, tidyr Suggests: knitr, testthat, rmarkdown License: MIT + file LICENSE MD5sum: 1f4c59fa6174cda720da11cbeed53b8e NeedsCompilation: no Package: Wrench Version: 1.16.0 Depends: R (>= 3.5.0) Imports: limma, matrixStats, locfit, stats, graphics Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR License: Artistic-2.0 MD5sum: fd3764fc865672c03c838108d6f5f263 NeedsCompilation: no Package: xcms Version: 3.20.0 Depends: R (>= 4.0.0), BiocParallel (>= 1.8.0), MSnbase (>= 2.21.4) Imports: mzR (>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics (>= 1.25.1), lattice, RColorBrewer, plyr, RANN, MassSpecWavelet (>= 1.5.2), S4Vectors, robustbase, IRanges, SummarizedExperiment, MsCoreUtils, MsFeatures Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>= 0.25.1), ncdf4, testthat, pander, magrittr, rmarkdown, multtest, MALDIquant, pheatmap, Spectra (>= 1.1.17), MsBackendMgf, progress, signal Enhances: Rgraphviz, rgl, XML License: GPL (>= 2) + file LICENSE MD5sum: 9bf832c553d287235f84417daf1aa2e7 NeedsCompilation: yes Package: xcore Version: 1.2.0 Depends: R (>= 4.2) Imports: DelayedArray (>= 0.18.0), edgeR (>= 3.34.1), foreach (>= 1.5.1), GenomicRanges (>= 1.44.0), glmnet (>= 4.1.2), IRanges (>= 2.26.0), iterators (>= 1.0.13), magrittr (>= 2.0.1), Matrix (>= 1.3.4), methods (>= 4.1.1), MultiAssayExperiment (>= 1.18.0), stats, S4Vectors (>= 0.30.0), utils Suggests: AnnotationHub (>= 3.0.2), BiocGenerics (>= 0.38.0), BiocParallel (>= 1.28), BiocStyle (>= 2.20.2), data.table (>= 1.14.0), devtools (>= 2.4.2), doParallel (>= 1.0.16), ExperimentHub (>= 2.2.0), knitr (>= 1.37), pheatmap (>= 1.0.12), proxy (>= 0.4.26), ridge (>= 3.0), rmarkdown (>= 2.11), rtracklayer (>= 1.52.0), testthat (>= 3.0.0), usethis (>= 2.0.1), xcoredata License: GPL-2 MD5sum: 4eff542ecdc60f951bdad3064aa977b1 NeedsCompilation: no Package: XDE Version: 2.44.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5) Imports: BiocGenerics, genefilter, graphics, grDevices, gtools, methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta, siggenes Suggests: MASS, RUnit Enhances: coda License: LGPL-2 MD5sum: e6790ad1ba031d70e124e5171c3f2211 NeedsCompilation: yes Package: Xeva Version: 1.14.0 Depends: R (>= 3.6) Imports: methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2, scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid, nlme, PharmacoGx, downloader Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: f7d2cb1d722ce8e8d5362f6cb028c4b1 NeedsCompilation: no Package: XINA Version: 1.16.0 Depends: R (>= 3.5) Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 50ff4a615fd8312da7035da4f9b70193 NeedsCompilation: no Package: xmapbridge Version: 1.56.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 MD5sum: 5ee17bb06422d3a3305879283372f926 NeedsCompilation: no Package: XNAString Version: 1.6.0 Depends: R (>= 4.1) Imports: utils, Biostrings, BSgenome, data.table, GenomicRanges, IRanges, methods, Rcpp, stringi, S4Vectors, future.apply, stringr, formattable, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, BSgenome.Hsapiens.UCSC.hg38, pander License: GPL-2 MD5sum: 5b98e220fe8cfb204c0615e28883d498 NeedsCompilation: yes Package: XVector Version: 0.38.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9) Imports: methods, utils, tools, zlibbioc, BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 MD5sum: 5a4445f2351e83d7d558449672465a02 NeedsCompilation: yes Package: yamss Version: 1.24.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.15.3), SummarizedExperiment Imports: IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table, grDevices, limma Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat License: Artistic-2.0 MD5sum: 2da0e264f86e6a2c11b82b0678271d9d NeedsCompilation: no Package: YAPSA Version: 1.24.0 Depends: R (>= 3.6.0), GenomicRanges, ggplot2, grid Imports: limSolve, SomaticSignatures, VariantAnnotation, GenomeInfoDb, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, doParallel, PMCMRplus, ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings, BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: d4a9864b6719e1de991f5a3b69fc2d22 NeedsCompilation: no Package: yarn Version: 1.24.0 Depends: Biobase Imports: biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro Suggests: knitr, rmarkdown, testthat (>= 0.8) License: Artistic-2.0 MD5sum: 7892c395b701000bd7e5e5285dd66409 NeedsCompilation: no Package: zellkonverter Version: 1.8.0 Imports: Matrix, basilisk, reticulate, SingleCellExperiment (>= 1.11.6), SummarizedExperiment, DelayedArray, methods, S4Vectors, utils, cli Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rmarkdown, rhdf5, scRNAseq, spelling, testthat, withr License: MIT + file LICENSE MD5sum: 71f3a2d185087edb14baa34f990a5892 NeedsCompilation: no Package: zenith Version: 1.0.2 Depends: R (>= 4.2.0), methods Imports: variancePartition (>= 1.26.0), limma, EnrichmentBrowser (>= 2.22.0), GSEABase (>= 1.54.0), msigdbr (>= 7.5.1), Rfast, ggplot2, tidyr, reshape2, progress, utils, Rdpack, stats Suggests: BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit License: Artistic-2.0 MD5sum: a4a3ea32743ae6b681c2af19ebf71693 NeedsCompilation: no Package: zFPKM Version: 1.20.0 Depends: R (>= 3.4.0) Imports: checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment Suggests: knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 688763d995e61d7e1e1e70f74efe8774 NeedsCompilation: no Package: zinbwave Version: 1.20.0 Depends: R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment Imports: BiocParallel, softImpute, stats, genefilter, edgeR, Matrix Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2 License: Artistic-2.0 MD5sum: c9bd83da434b47fc7c0ebf87a6ea78e1 NeedsCompilation: no Package: zlibbioc Version: 1.44.0 License: Artistic-2.0 + file LICENSE MD5sum: dc1ace66ffe17c1512715b7d8271f093 NeedsCompilation: yes