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VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 51942d3a3089fd86bb9523326930d36a NeedsCompilation: yes Package: AnnotationHubData Version: 1.26.1 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: 7af5251e67d3e3c8a2f899a23262d3ed NeedsCompilation: no Package: annotationTools Version: 1.70.0 Imports: Biobase, stats Suggests: BiocStyle License: GPL MD5sum: 871a1964e3d11fe35e19b2c25a61d2bb NeedsCompilation: no Package: annotatr Version: 1.22.0 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: 9015c0315c7705302cf10635826646be NeedsCompilation: no Package: anota Version: 1.44.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 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methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr, dplyr, lubridate, plotly, ggplot2 Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: bcbefba9776f07db017fbd4aaf8944e1 NeedsCompilation: no Package: AnVILPublish Version: 1.6.0 Imports: AnVIL, httr, jsonlite, rmarkdown, yaml, readr, whisker, tools, utils, stats Suggests: knitr, BiocStyle, BiocManager, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 1fe612f55f42351ab9fee715609ae161 NeedsCompilation: no Package: APAlyzer Version: 1.10.0 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: bb8744f645ffdaa03f9b62c005307f93 NeedsCompilation: no Package: apComplex Version: 2.62.0 Depends: R (>= 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PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat License: GPL (>= 3) + file LICENSE MD5sum: 0076d69f58f85fd6281ba03bcba8bbae NeedsCompilation: no Package: ASAFE Version: 1.22.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 MD5sum: eaa60da746e1f05badd64301db839827 NeedsCompilation: no Package: ASEB Version: 1.40.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) MD5sum: 4f0c377f0d6df54dd9ef043cc30fab39 NeedsCompilation: yes Package: ASGSCA Version: 1.30.0 Imports: Matrix, MASS Suggests: BiocStyle License: GPL-3 MD5sum: 4164abc4e3cd8351c009d04851c6877f NeedsCompilation: no Package: ASICS Version: 2.12.1 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: 0f76deaba7e73c2332357db448607eff NeedsCompilation: no 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stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 2b2c07c21f53815f147803b1a8f4ef30 NeedsCompilation: no Package: ASSET Version: 2.14.0 Depends: R (>= 3.5.0), stats, graphics Imports: MASS, msm, rmeta Suggests: RUnit, BiocGenerics, knitr License: GPL-2 + file LICENSE MD5sum: 9dd6e62f38ac9f3c6b486db341db7afa NeedsCompilation: no Package: ASSIGN Version: 1.32.0 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: 85171efb98ea4c0b52d6f981827fdca5 NeedsCompilation: no Package: ASURAT Version: 1.0.0 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: fbc1187e5ecb6c0557c0fb42cde3f0e8 NeedsCompilation: yes Package: ATACseqQC Version: 1.20.2 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: 1a070d58462b5816efa6ab289a59a84f NeedsCompilation: no Package: atena Version: 1.2.2 Depends: R (>= 4.1), SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, BiocParallel, S4Vectors, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, scales Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit 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NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, rbokeh, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: 787c2fed47888090106c92ee706e4a97 NeedsCompilation: no Package: autonomics Version: 1.4.0 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: 5206ba0c92fe0e5a902cbeb9c616f2f6 NeedsCompilation: no Package: AWFisher Version: 1.10.0 Depends: R (>= 3.6) Imports: edgeR, 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License: Artistic-2.0 MD5sum: 7dc6638e1c77c84e6e6b00e41ba0de02 NeedsCompilation: no Package: bambu Version: 2.2.0 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, apeglm, utils, DEXSeq Enhances: parallel License: GPL-3 + file LICENSE MD5sum: 1acfbe47f4f6c70d864e8def8134e9a4 NeedsCompilation: yes Package: bamsignals Version: 1.28.0 Depends: R (>= 3.5.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 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ggplot2, BiocGenerics, gtools, doParallel, foreach Suggests: knitr, BiocStyle, testthat License: file LICENSE MD5sum: 288cde8cae5d98b933b18e5f0a9274e7 NeedsCompilation: no Package: brendaDb Version: 1.10.0 Imports: dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel, crayon, utils, tidyr, curl, xml2, grDevices, rlang, BiocFileCache, rappdirs LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, devtools License: MIT + file LICENSE MD5sum: aa75abf05805dfc4dbc49a450f28278d NeedsCompilation: yes Package: BRGenomics Version: 1.8.0 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: 0b7809e8b02928596ff43c1a6416f6a1 NeedsCompilation: no Package: bridge Version: 1.60.0 Depends: R (>= 1.9.0), rama License: GPL (>= 2) 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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: 3547bb1a2b0543e4f63033334176ca09 NeedsCompilation: no Package: bsseq Version: 1.32.0 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, 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BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 89ed8db5c8ca853b5a551331dda23105 NeedsCompilation: no Package: BUS Version: 1.52.0 Depends: R (>= 2.3.0), minet Imports: stats, infotheo License: GPL-3 MD5sum: d8ed38674ed27e6fba61b3fb0bd38ce7 NeedsCompilation: yes Package: BUScorrect Version: 1.14.0 Depends: R (>= 3.5.0) Imports: gplots, methods, grDevices, stats, SummarizedExperiment Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 4e0d375f3a5d0edb8403d8924b8812d3 NeedsCompilation: yes Package: BUSpaRse Version: 1.10.0 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, 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S4Vectors, scales, scater, stats Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot License: GPL (>= 2) MD5sum: 0819be1ea4e7df4036ff58b15d54fe61 NeedsCompilation: no Package: Category Version: 2.62.0 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: acf047c29150009d586de670292f2da7 NeedsCompilation: no Package: categoryCompare Version: 1.40.0 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: 1b9534d76fbb8b257d1cdf10b354de53 NeedsCompilation: no Package: CausalR Version: 1.28.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 005ffd41199596aee0e66f7826b1940a NeedsCompilation: no Package: cbaf Version: 1.18.4 Depends: R (>= 4.1) Imports: BiocFileCache, RColorBrewer, cBioPortalData, genefilter, gplots, grDevices, stats, utils, openxlsx Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 1a16122745e3ba477dcbe02242b98b92 NeedsCompilation: no Package: CBEA Version: 1.0.0 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: 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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: e03954a5a440248855a9400067c90e59 NeedsCompilation: yes Package: ccmap Version: 1.22.0 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: a36a95460b96618be632289e5bd83650 NeedsCompilation: no Package: CCPROMISE Version: 1.22.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: 58952c0eaea1b03085c7a864958afa60 NeedsCompilation: no Package: ccrepe Version: 1.32.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat License: MIT + 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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: 5a939299bf847ff4c14b3516ef4b6ea0 NeedsCompilation: no Package: ChIPanalyser Version: 1.18.0 Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb Suggests: BSgenome.Dmelanogaster.UCSC.dm3,knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 6206bf6fc2d7aa9eecf3bc9e8e807586 NeedsCompilation: no Package: ChIPComp Version: 1.26.0 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: 683c78aa338e80925d931bfa15495e14 NeedsCompilation: yes Package: chipenrich 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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: 6c598b577403b3ab095d7ccc90f3eee0 NeedsCompilation: yes Package: conumee Version: 1.30.0 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: 2000d703b3e3cfbb94f878d15d9d35ba NeedsCompilation: no Package: convert Version: 1.72.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL MD5sum: c66659ab13a6474d096571e4737790bc NeedsCompilation: no Package: copa Version: 1.64.0 Depends: Biobase, methods Suggests: 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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: 3cb957c80c1b71dbb6a61cb88e0d3210 NeedsCompilation: no Package: cytoKernel Version: 1.2.0 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: b1db75f53d7be399b39579c55b03519c NeedsCompilation: yes Package: cytolib Version: 2.8.0 Depends: R (>= 3.4) Imports: RcppParallel, RProtoBufLib LinkingTo: Rcpp, BH(>= 1.75.0.0), RProtoBufLib(>= 2.3.5),Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1) Suggests: knitr, rmarkdown License: file LICENSE License_restricts_use: yes MD5sum: c523b7c40f12ab266d38f87da867b1d0 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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: 865b1c8ed95cfe063e1146da29d2f6e1 NeedsCompilation: no Package: DaMiRseq Version: 2.8.0 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: 0657d15b6616d3eac788768f1b6ac764 NeedsCompilation: no Package: DAPAR Version: 1.28.5 Depends: R (>= 4.2.0) Imports: Biobase, MSnbase, DAPARdata (>= 1.26.3), 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: 5924caae647f2a16a0abbbbf314c197f NeedsCompilation: no Package: DART Version: 1.44.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: 45831961934ac910c93d6840e3ce53f3 NeedsCompilation: no Package: dasper Version: 1.6.0 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: 4adc5d8309acab4dafaa660a1cc52087 NeedsCompilation: no Package: dcanr Version: 1.12.0 Depends: R (>= 3.6.0) Imports: igraph, foreach, plyr, stringr, reshape2, methods, Matrix, graphics, stats, RColorBrewer, circlize, doRNG Suggests: EBcoexpress, testthat, EBarrays, GeneNet, COSINE, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 MD5sum: 2600ba8971f14227332532b772be30a6 NeedsCompilation: no Package: dce Version: 1.4.99 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: 450294d13364ddc48a3c028f1a5a465f NeedsCompilation: no Package: dcGSA Version: 1.24.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: b6387d4c4e8efde5d55fe25efe64de34 NeedsCompilation: no Package: ddCt Version: 1.52.0 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: 603fd462faabfa5db097225d4f24c1ab NeedsCompilation: no Package: ddPCRclust Version: 1.16.0 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: e15108fc24564b00958ed5b1b5ec8528 NeedsCompilation: no Package: dearseq Version: 1.8.4 Depends: R (>= 3.6.0) Imports: CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr, matrixStats, methods, patchwork, parallel, pbapply, reshape2, rlang, 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: 488ae173b60c5de2e74af76f8eb72b0a NeedsCompilation: no Package: debCAM Version: 1.14.0 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: ebef90043bfff1be4868635260f94034 NeedsCompilation: no Package: debrowser Version: 1.24.1 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: b9209746971f31549408fae3fdc1a16c NeedsCompilation: no Package: DECIPHER Version: 2.24.0 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: c4a735fd8fb2d99d179139a57781b6c8 NeedsCompilation: yes Package: deco Version: 1.12.0 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: 1962d229c159302647c2229deaa8e252 NeedsCompilation: no Package: DEComplexDisease Version: 1.16.0 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: 49fcef279e5ad6e3a338df7e2364cfcd NeedsCompilation: yes Package: decompTumor2Sig Version: 2.12.0 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: 8c2236cc1763123d86b639d771269b3b NeedsCompilation: no Package: 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License: GPL (>= 2.0) MD5sum: 7c16c3f2e23026b9e3daabecafbbcb6a NeedsCompilation: no Package: DeepPINCS Version: 1.4.0 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: d08e323eb2bcf3d001a59213d9974d1a NeedsCompilation: no Package: deepSNV Version: 1.42.1 Depends: R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.13.44), Imports: Rhtslib LinkingTo: Rhtslib (>= 1.13.1) Suggests: RColorBrewer, knitr, rmarkdown License: GPL-3 MD5sum: 16cc673ea1b75b40b77daf9bc13e708e NeedsCompilation: yes Package: DEFormats Version: 1.24.0 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: 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cluster, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, lasso2, magrittr, Nozzle.R1, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE MD5sum: 54d137c5ae5beafadff7fcfc0566f55b NeedsCompilation: no Package: DEGseq Version: 1.50.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: 1f49f0b750e56d388478d1d0a09a63ac NeedsCompilation: yes Package: DelayedArray Version: 0.22.0 Depends: R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>= 0.37.0), 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: d9627acc6dbdfd8fbfc488b34a31b4dd NeedsCompilation: yes Package: DelayedDataFrame Version: 1.12.0 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: 484367b33f5996446cdb93662b6a7b76 NeedsCompilation: no Package: DelayedMatrixStats Version: 1.18.2 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: f77477c555d4cbd119c9734e1d21e2eb NeedsCompilation: no Package: DelayedRandomArray Version: 1.4.0 Depends: DelayedArray Imports: methods, dqrng, Rcpp LinkingTo: dqrng, BH, Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, Matrix License: GPL-3 MD5sum: ff40ba0dd030f377369953b90f1541b7 NeedsCompilation: yes Package: DelayedTensor Version: 1.2.0 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: 691432f082733fae2567f208af4d597b NeedsCompilation: no Package: deltaCaptureC Version: 1.10.0 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2, tictoc Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: c8e9ccc12167d7b158dca455937458a9 NeedsCompilation: no Package: deltaGseg Version: 1.36.0 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 MD5sum: b6dc73ad7af9189ce4cbe5231dc175d0 NeedsCompilation: no Package: DeMAND Version: 1.26.0 Depends: R (>= 2.14.0), KernSmooth, methods License: file LICENSE MD5sum: 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2d2ff07071493c4d00106561de61b524 NeedsCompilation: no Package: DEqMS Version: 1.14.0 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: e04a078593af4dba35c6ad5c2de0ad89 NeedsCompilation: no Package: derfinder Version: 1.30.0 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: 831d7dbc72c0a28136e4c6ebab106f6e NeedsCompilation: no Package: derfinderHelper Version: 1.30.0 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: fa3f435a1cc0c466fec50347e0e4d8e3 NeedsCompilation: no Package: derfinderPlot Version: 1.30.0 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: fc4f92ba5d1bb96e788ffc97ca972526 NeedsCompilation: no Package: DEScan2 Version: 1.16.0 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: 8ad7dfce9760be85736008d033b2cdad NeedsCompilation: yes Package: DESeq2 Version: 1.36.0 Depends: S4Vectors (>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter, 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 (>= 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ggplot2, matrixStats, Sushi, edgeR, locfit, statmod, biomaRt, GenomeInfoDb, S4Vectors, IRanges, grDevices, graphics, stats, utils, Biobase, readr, data.table, rtracklayer, pbapply, limma Suggests: DESeq2, diffloopdata, ggrepel, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: df25a4fe701aaf3171a546b2354fc56c NeedsCompilation: no Package: diffuStats Version: 1.16.0 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: 9ff123fad97b3b3b2b88e3fb6386fe2e NeedsCompilation: yes Package: diffUTR Version: 1.4.0 Depends: R (>= 4.0) Imports: S4Vectors, SummarizedExperiment, limma, edgeR, DEXSeq, GenomicRanges, Rsubread, ggplot2, rtracklayer, ComplexHeatmap, ggrepel, stringi, methods, stats, GenomeInfoDb, dplyr, matrixStats, IRanges, 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ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown License: Artistic-2.0 MD5sum: 183e14ce2851998bbde09cf80e63a00e NeedsCompilation: no Package: enrichplot Version: 1.16.2 Depends: R (>= 3.5.0) Imports: aplot, DOSE (>= 3.16.0), ggplot2, ggraph, graphics, grid, igraph, methods, plyr, purrr, RColorBrewer, reshape2, 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, ggnewscale, ggrepel (>= 0.9.0), ggstar, treeio, scales, tidytree, rlang, ggtreeExtra, tidydr License: Artistic-2.0 MD5sum: fdea16fdc00fa128121830c4a0e3b8c4 NeedsCompilation: no Package: enrichTF Version: 1.12.0 Depends: pipeFrame Imports: BSgenome, rtracklayer, motifmatchr, TFBSTools, R.utils, methods, JASPAR2018, GenomeInfoDb, 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graph, mnem, latex2exp Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db License: GPL-3 MD5sum: 5e5d5fd897d68e5752c37d5c5fc473b5 NeedsCompilation: no Package: epistack Version: 1.2.0 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: 52b920a6ebf511b0077839a4331e4e27 NeedsCompilation: no Package: EpiTxDb Version: 1.8.0 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, 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utils, KernSmooth, lattice, ks, RColorBrewer, rrcov, corpcor, mnormt Suggests: xtable, testthat, openCyto, ggcyto, ggridges Enhances: RBGL,graph License: Artistic-2.0 MD5sum: e586eb8b37993393ac0e54db5c5704f5 NeedsCompilation: no Package: flowTime Version: 1.20.0 Depends: R (>= 3.4), flowCore Imports: utils, dplyr (>= 1.0.0), tibble, magrittr, plyr, rlang Suggests: knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, stats, flowClust, openCyto, flowStats, ggcyto License: Artistic-2.0 MD5sum: 72d6b024e2f8ec4cf07e1f058e490ca6 NeedsCompilation: no Package: flowTrans Version: 1.48.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 MD5sum: 1c3a8908b06a2570288196e9b75c3dcc NeedsCompilation: no Package: flowUtils Version: 1.59.0 Depends: R (>= 2.2.0) Imports: Biobase, graph, methods, stats, utils, corpcor, RUnit, XML, flowCore (>= 1.32.0) Suggests: gatingMLData License: Artistic-2.0 MD5sum: 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2.1.1), ncdfFlow(>= 2.25.4), DelayedArray, S4Vectors LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib (>= 2.3.7),Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1) Suggests: testthat, flowWorkspaceData (>= 2.23.2), knitr, rmarkdown, ggcyto, parallel, CytoML, openCyto License: file LICENSE License_restricts_use: yes MD5sum: ec8490d7e63275639ff36b4519a055fe NeedsCompilation: yes Package: fmcsR Version: 1.38.0 Depends: R (>= 2.10.0), ChemmineR, methods Imports: RUnit, methods, ChemmineR, BiocGenerics, parallel Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap,rmarkdown License: Artistic-2.0 MD5sum: a24226bc9bf9cb5b94758dfd763f087e NeedsCompilation: yes Package: fmrs Version: 1.6.0 Depends: R (>= 4.1.0) Imports: methods, survival, stats Suggests: BiocGenerics, testthat, knitr, utils License: GPL-3 MD5sum: 13878f9bd54ab6e753aa687f6c3ea9ee NeedsCompilation: yes Package: fobitools Version: 1.4.0 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: 1006b63802e24e9b472b3a79cc122e5b NeedsCompilation: no Package: FoldGO Version: 1.14.0 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: decdf72e0298983e0479e93104685bc8 NeedsCompilation: no Package: FRASER Version: 1.8.1 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, 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matrixStats, minfi, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb, grDevices, graphics, stats Suggests: prettydoc, minfiData, knitr, rmarkdown License: GPL-3 MD5sum: e25c4d8cbf81b53115ea464cf71b6b2e NeedsCompilation: no Package: GA4GHclient Version: 1.20.0 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: 960dedf7d58c03f80a0e296f04bc9bcc NeedsCompilation: no Package: GA4GHshiny Version: 1.18.0 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: 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dplyr, magrittr, data.table, igraph, graph, RBGL, GO.db, org.Hs.eg.db, org.Mm.eg.db, GOSemSim, GEOquery, AnnotationDbi, Biobase, BiocFileCache, matrixStats Suggests: org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Dr.eg.db, org.Ce.eg.db, org.At.tair.db, org.EcK12.eg.db, org.Bt.eg.db, org.Cf.eg.db, org.Ag.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Pt.eg.db, org.Pf.plasmo.db, org.Mmu.eg.db, org.Ss.eg.db, org.Xl.eg.db, testthat, pryr, knitr, rmarkdown, prettydoc, ggplot2, kableExtra, profvis, reshape2 License: MIT + file LICENSE MD5sum: 5b518703b3dfe6000b825e4d2fb53759 NeedsCompilation: no Package: GAprediction Version: 1.22.0 Depends: R (>= 3.3) Imports: glmnet, stats, utils, Matrix Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: e31d12cd88a7e359a88e9da75c74b1ec NeedsCompilation: no Package: garfield Version: 1.24.0 Suggests: knitr License: GPL-3 MD5sum: df020cadf46efef93f423565afbc0367 NeedsCompilation: yes Package: GARS Version: 1.16.0 Depends: R (>= 3.5), ggplot2, cluster 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BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: GPL-3 MD5sum: 831ab2337b4ac899429e3b163f5fb95a NeedsCompilation: no Package: gcatest Version: 1.26.0 Depends: R (>= 3.2) Imports: lfa Suggests: knitr, ggplot2 License: GPL-3 MD5sum: ea717ba8c0c92fdfc2d70faf1ddcfda7 NeedsCompilation: yes Package: gCrisprTools Version: 2.2.2 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: ca5cc1152e0d91efe929a3ad6e765fd8 NeedsCompilation: no Package: gcrma Version: 2.68.0 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, 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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: f7b1a331dd83fc41e1d4774fb4f0626a NeedsCompilation: no Package: GDSArray Version: 1.16.0 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: d7dd09917a4090cb702be151e305cc30 NeedsCompilation: no Package: gdsfmt Version: 1.32.0 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics License: LGPL-3 MD5sum: 938410df440481a12b1bddab82be501e NeedsCompilation: yes Package: GEM Version: 1.22.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown License: Artistic-2.0 MD5sum: fff17f0e4fe8e25f8033ae4140bf325d NeedsCompilation: no Package: gemini Version: 1.10.0 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: 3038691663eaebf2d18b87ed38f129de NeedsCompilation: no Package: genArise Version: 1.72.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: c58a551749cac54942dce9c7d257b3a8 NeedsCompilation: no Package: genbankr Version: 1.24.0 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: 07aaeade0aa2a4f5bcca771e4e09b0d9 NeedsCompilation: no Package: GeneAccord Version: 1.14.0 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: c0a29dcf57805564ca4cff803cd9f7c5 NeedsCompilation: no Package: geneAttribution Version: 1.22.0 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: a1d4fdae452f51c4c79b33a9507bb30d NeedsCompilation: no Package: GeneBreak Version: 1.26.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: 84befe93fb4cc07a189426edfd32455f NeedsCompilation: no Package: geneClassifiers Version: 1.20.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: 191b2cf2274b03b01a3105256ceef106 NeedsCompilation: no Package: GeneExpressionSignature Version: 1.42.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: e8a332f39a02b85dd801a33e140776d9 NeedsCompilation: no Package: genefilter Version: 1.78.0 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: 982948da9c888610ef9da6172189494a NeedsCompilation: yes Package: genefu Version: 2.28.0 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: 1d45c6f0536d1a610587c1264383cc9c NeedsCompilation: no Package: GeneGA Version: 1.46.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: cefd73fa542da73f5ff1489585c2b268 NeedsCompilation: no Package: GeneGeneInteR Version: 1.22.0 Depends: R (>= 4.0) Imports: snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods License: GPL (>= 2) MD5sum: 9e4d904ec64dddcaa8bc60fbb702e326 NeedsCompilation: yes Package: GeneMeta Version: 1.68.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: 4852fbd6f1b1c14d86851a9ab37303c9 NeedsCompilation: no Package: GeneNetworkBuilder Version: 1.38.0 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 License: GPL (>= 2) MD5sum: b07c91144667db755fe11f0ecfce415a NeedsCompilation: yes Package: GeneOverlap Version: 1.32.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: a968a2c53375871c4137cffd9fabf22c NeedsCompilation: no Package: geneplast Version: 1.22.0 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.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: b7a7868eda8b86baa1134c9414c7359e NeedsCompilation: no Package: geneplotter Version: 1.74.0 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: d2467109ac0babeceed8a63d4d61098d NeedsCompilation: no Package: geneRecommender Version: 1.68.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: 6e59b1071f9719302ae63dc574e74ec5 NeedsCompilation: no Package: GeneRegionScan Version: 1.52.0 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: 82b285ef7845d073a1072d11a8914abc NeedsCompilation: no Package: geneRxCluster Version: 1.32.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: ddc12699b0a2919a7d90d69cdc9b00dc NeedsCompilation: yes Package: GeneSelectMMD Version: 2.40.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: 6cdd72bbe0bf8e7ea14b38a3882db717 NeedsCompilation: yes Package: GENESIS Version: 2.26.0 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: 05d23e887c6b241e1ed84e7bf4f568b8 NeedsCompilation: yes Package: GeneStructureTools Version: 1.16.0 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: 7772503edb24bb7e2426b155a91f901f NeedsCompilation: no Package: geNetClassifier Version: 1.36.0 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: 6fa1e77e0cc34fa2666d7e2d5c587d79 NeedsCompilation: no Package: GeneticsPed Version: 1.58.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: 0959ef64a51a1226d3e11023b19633cb NeedsCompilation: yes Package: GeneTonic Version: 2.0.2 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: 6ed9de63c115764a0fe1585b023abcc1 NeedsCompilation: no Package: geneXtendeR Version: 1.22.0 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: 2ac9660e9d1625591ff96502f7ce3759 NeedsCompilation: yes Package: GENIE3 Version: 1.18.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods License: GPL (>= 2) MD5sum: 4cf408c99fad63aac6384f80b65fc83a NeedsCompilation: yes Package: genoCN Version: 1.48.0 Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: 5f0db72d8153350357a45d2e968c7595 NeedsCompilation: yes Package: genomation Version: 1.28.0 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: 9844a84bf618e2ff8143b80afc77e7d9 NeedsCompilation: yes Package: GenomeInfoDb Version: 1.32.4 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: ea2f1b1fd9237a45254daf13e4ef6298 NeedsCompilation: no Package: genomeIntervals Version: 1.52.0 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: 202b0dd02ed7eae643e38d1082236cad NeedsCompilation: no Package: genomes Version: 3.26.0 Depends: readr, curl License: GPL-3 MD5sum: d00a1cef5a73ef396a7b47574e321e0c NeedsCompilation: no Package: GenomicAlignments Version: 1.32.1 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: f52948ea89d1b6c9bf9a1513e9406114 NeedsCompilation: yes Package: GenomicDataCommons Version: 1.20.3 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: 17731e25a4155421372c5e92719266d5 NeedsCompilation: no Package: GenomicDistributions Version: 1.4.6 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: fb79edc8e353e98c2ec7af6bf5f746f7 NeedsCompilation: no Package: GenomicFeatures Version: 1.48.4 Depends: R (>= 3.5.0), BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29), IRanges (>= 2.13.23), GenomeInfoDb (>= 1.25.7), 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 License: Artistic-2.0 MD5sum: e3332b86b772f8a382e0bc1381063fa9 NeedsCompilation: no Package: GenomicFiles Version: 1.32.1 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: 136282500764ce57ad5054ba24bad27b NeedsCompilation: no Package: genomicInstability Version: 1.2.0 Depends: R (>= 4.1.0), checkmate Imports: mixtools, SummarizedExperiment Suggests: SingleCellExperiment, ExperimentHub, pROC License: file LICENSE MD5sum: eae22efeef71ac36f8624894974ed348 NeedsCompilation: no Package: GenomicInteractionNodes Version: 1.0.0 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: 0a2a769f1ec537c759048f2db24f2f70 NeedsCompilation: no Package: GenomicInteractions Version: 1.30.0 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: 96659ea221c4f64b249228789fd78fca NeedsCompilation: no Package: GenomicOZone Version: 1.10.0 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: d964f75c230541af7be2fecf606cbc90 NeedsCompilation: no Package: GenomicRanges Version: 1.48.0 Depends: R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), 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: 98398fd94d284583e784608cb404c7cb NeedsCompilation: yes Package: GenomicScores Version: 2.8.2 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: e152a0edfcad2975796dafe24ee7c9df NeedsCompilation: no Package: GenomicSuperSignature Version: 1.4.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable 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: 38aa4dcea080b0ab5b569ff284b27e97 NeedsCompilation: no Package: GenomicTuples Version: 1.30.0 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: b8a53c37b525dc2fe9cceb7c44cdbf05 NeedsCompilation: yes Package: genotypeeval Version: 1.28.0 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: b6aea54dff2611236c0c439ce54bc4e8 NeedsCompilation: no Package: genphen Version: 1.24.0 Depends: R (>= 3.5.0), Rcpp (>= 0.12.17), methods, stats, graphics Imports: rstan (>= 2.17.3), ranger, parallel, foreach, doParallel, e1071, Biostrings, rPref Suggests: testthat, ggplot2, gridExtra, ape, ggrepel, knitr, reshape, xtable License: GPL (>= 2) MD5sum: d6019b69c0ce4be37102c0883b9a0f05 NeedsCompilation: no Package: GenProSeq Version: 1.0.0 Depends: keras, mclust, R (>= 4.2) Imports: tensorflow, word2vec, DeepPINCS, ttgsea, CatEncoders, reticulate, stats Suggests: knitr, testthat, rmarkdown 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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: Artistic-2.0 MD5sum: b311055f5173b8cd8874ef244b30a0e1 NeedsCompilation: no Package: ggmanh Version: 1.0.0 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: 65d0f00ed391070b517452cfbc7772ee NeedsCompilation: no Package: ggmsa Version: 1.2.3 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 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License: Artistic-2.0 MD5sum: 7827057246298d74c1b37d57794dc002 NeedsCompilation: no Package: infercnv Version: 1.12.0 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, leiden, reshape, rjags, fitdistrplus, future, foreach, doParallel, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse Suggests: BiocStyle, knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 9c5c6197fccb5e3dca5e082d2cf0491d NeedsCompilation: no Package: infinityFlow Version: 1.6.0 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: 548553d6e6f81b0bef3846e5ab4ed86c 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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: 45a851aaebde81e80a7783d6c8e7a1b1 NeedsCompilation: no Package: interactiveDisplay Version: 1.34.0 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: e14b460dd17885e9bbf494e461b85410 NeedsCompilation: no Package: interactiveDisplayBase Version: 1.34.0 Depends: R (>= 2.10), 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(>= 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: 35b6df25f577ec17181c627ee57688ef NeedsCompilation: yes Package: ISAnalytics Version: 1.6.2 Depends: R (>= 4.2), magrittr Imports: utils, dplyr, readr, tidyr, purrr, rlang, tibble, BiocParallel, stringr, fs, lubridate, lifecycle, ggplot2, ggrepel, stats, psych, data.table, readxl, tools, Rcapture, grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib Suggests: testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown, roxygen2, vegan, withr, extraDistr, ggalluvial, scales, gridExtra, R.utils, RefManageR, flexdashboard, DT, circlize, plotly, gtools, eulerr, openxlsx License: CC BY 4.0 MD5sum: 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methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: 8b31c8bd16733bee908b9b99bcff267d NeedsCompilation: no Package: methylCC Version: 1.10.0 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: 7b17a86924421298ca249f7532a9384f NeedsCompilation: no Package: methylclock Version: 1.2.1 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: 4df9eb72fe445ff758e88537307a305f NeedsCompilation: yes Package: methylGSA Version: 1.14.0 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: f207622cc9659a8130a5eaa4b4ca24fd NeedsCompilation: no Package: methylInheritance Version: 1.20.0 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: a8b38b583fe6af051b26b1b11af8e8c7 NeedsCompilation: no Package: methylKit Version: 1.22.0 Depends: R (>= 3.5.0), 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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: 4ede0bcbe8a42a4438e4acd9d063fa47 NeedsCompilation: yes Package: methylscaper Version: 1.4.0 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: b4e28dafeaab2b201714f733d1dd01fd NeedsCompilation: no Package: MethylSeekR Version: 1.36.0 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), 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c3ad772006e2598ca259eb5f832c5d43 NeedsCompilation: no Package: microbiomeMarker Version: 1.2.2 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: 26fa0e67fc8484efe5a118ec990526bf NeedsCompilation: no Package: MicrobiomeProfiler Version: 1.2.0 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: 8fd3d3eeda46d4c0462603167dc91637 NeedsCompilation: no 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Rcpp, org.Hs.eg.db, SPONGE, foreach, doParallel Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: c6dce0f7dbd8145455a153d484b7cf49 NeedsCompilation: yes Package: mirTarRnaSeq Version: 1.4.0 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: 4006d813211710957b6e3075b2d7a60a NeedsCompilation: no Package: missMethyl Version: 1.30.0 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, 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a968c30666fe9fc4c1dd47b5be3435f3 NeedsCompilation: no Package: MMUPHin Version: 1.10.3 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: e7062d9e440553e5d5933f899a0f8d71 NeedsCompilation: no Package: mnem Version: 1.12.0 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: fb9a655cf6ad1ad9397c78850752c82a NeedsCompilation: yes Package: moanin Version: 1.4.0 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: 3717d2071e355c4797e1209b86f888e4 NeedsCompilation: no Package: MobilityTransformR Version: 1.0.0 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: e2578b9000852c456ce74feef80dc0e2 NeedsCompilation: no Package: MODA Version: 1.22.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 17856d68be4e530d330bfe545f63b1d5 NeedsCompilation: no Package: ModCon Version: 1.4.0 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: 7082cff7ac8851cdcf95df8445788cb6 NeedsCompilation: no Package: Modstrings Version: 1.12.1 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: 84fa10fdde56d16c30d916672f9feb6f NeedsCompilation: no Package: MOFA2 Version: 1.6.0 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: GPL (>= 2) + file LICENSE MD5sum: d7f68a5b04da0d1eda0bd4e2ffa02716 NeedsCompilation: yes Package: MOGAMUN Version: 1.6.0 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: knitr, markdown License: GPL-3 + file LICENSE MD5sum: 8aec47b4e151b0258d5b528d5c53507b NeedsCompilation: no Package: mogsa Version: 1.30.0 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: 612d76cda941c07e8e633ccf483860be NeedsCompilation: no Package: MOMA Version: 1.8.0 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: 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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: 07a95b36befabeaba5f5734d5b247343 NeedsCompilation: yes Package: MoonlightR Version: 1.22.0 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: d941a05dbdd0de77ad8d965c6b0bc8bd NeedsCompilation: no Package: mosaics Version: 2.34.0 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: 3a79e57c4fa10f44de145b3d85e24f13 NeedsCompilation: yes Package: mosbi Version: 1.2.0 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: 373f1b9a03e2358e40495637aa20384c NeedsCompilation: yes Package: MOSim Version: 1.10.0 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: 37fabb53e25f96459c01237d9c709610 NeedsCompilation: no Package: Motif2Site Version: 1.0.0 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: 289ae8a1053d2cbab94a569150f43041 NeedsCompilation: no Package: motifbreakR Version: 2.10.2 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.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP142.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle License: GPL-2 MD5sum: 4fe3e984afe8dd8a3d4ee4980ff17553 NeedsCompilation: no Package: motifcounter Version: 1.20.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: 12fa460cb595d003cc95da5faf0b3848 NeedsCompilation: yes 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MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020 License: GPL (>= 2) MD5sum: b294cb36d9c2129b9fe4bd7d3064b8fb NeedsCompilation: no Package: MouseFM Version: 1.6.0 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: 05ac86dd893db57e72256797232f8776 NeedsCompilation: no Package: MPFE Version: 1.32.0 License: GPL (>= 3) MD5sum: fe9566380298c101420044e47142a906 NeedsCompilation: no Package: mpra Version: 1.18.0 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: 49fffac9b09624438114b012ef286509 NeedsCompilation: no Package: MPRAnalyze Version: 1.14.0 Imports: BiocParallel, methods, progress, stats, SummarizedExperiment 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stringi LinkingTo: Rcpp, RcppThread Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle License: MIT + file LICENSE MD5sum: 2880dd84e35031a23944f9eca2b1e58e NeedsCompilation: yes Package: MsBackendMassbank Version: 1.4.0 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: b94e2da9751372a59ad1ee97cdc37209 NeedsCompilation: no Package: MsBackendMgf Version: 1.4.0 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: e670010c2821dfc46b71e39c7a0770dc NeedsCompilation: no Package: MsBackendMsp Version: 1.0.0 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: d8a6c351f902ea1ab551fd454e423f9b NeedsCompilation: no Package: MsBackendRawFileReader Version: 1.2.0 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: e2f0b22e3fbbb564e11a9e5f4bd37c82 NeedsCompilation: yes Package: MsCoreUtils Version: 1.8.0 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 License: Artistic-2.0 MD5sum: 817486ce7a307ad13ce81846bdfe1e29 NeedsCompilation: yes Package: MsFeatures Version: 1.4.0 Depends: R (>= 4.1) Imports: methods, ProtGenerics (>= 1.23.5), 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ggplot2, DBI, RSQLite Suggests: MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL License: GPL-3 + file LICENSE MD5sum: efb5a036979bb3caac71030dabb998f8 NeedsCompilation: no Package: msqrob2 Version: 1.4.0 Depends: R (>= 4.1), QFeatures (>= 1.1.2) Imports: stats, methods, lme4, purrr, BiocParallel, Matrix, MASS, limma, SummarizedExperiment, codetools Suggests: multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata, MSnbase, matrixStats, MsCoreUtils License: Artistic-2.0 MD5sum: b201528d28e52aab108022f507d671d2 NeedsCompilation: no Package: MSstats Version: 4.4.1 Depends: R (>= 4.0) Imports: MSstatsConvert, data.table, checkmate, MASS, limma, lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel, gplots, marray, stats, grDevices, graphics, methods LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, tinytest, covr, markdown License: Artistic-2.0 MD5sum: 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MSstats Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 921b671d9e06100b4ae89be1ff06a92a NeedsCompilation: no Package: MSstatsTMT Version: 2.4.1 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: 03d1d23a12e1e36fa35096d4943efa39 NeedsCompilation: no Package: MuData Version: 1.0.0 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: e36279a6f823450164cb00e1df4246c8 NeedsCompilation: no Package: Mulcom Version: 1.46.0 Depends: R (>= 2.10), Biobase Imports: graphics, grDevices, stats, methods, fields License: GPL-2 MD5sum: 7ca618d3ec247e08d48841182fed4b8b 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BiocStyle, RaggedExperiment License: file LICENSE MD5sum: 72232fab809177bb0b36b2f725b5fc69 NeedsCompilation: no Package: multiGSEA Version: 1.6.0 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: 0910d0d94dfe040301ba931fb6e995a8 NeedsCompilation: no Package: multiHiCcompare Version: 1.14.0 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: 9685d6b4a62a8895fa5015e3784e6679 NeedsCompilation: no Package: MultiMed Version: 2.18.0 Depends: R (>= 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License: GPL-3 MD5sum: d76fe170b7824f50d48c0f6847eb63ca NeedsCompilation: no Package: MungeSumstats Version: 1.4.5 Depends: R(>= 4.1) Imports: magrittr, data.table, utils, R.utils, dplyr, stats, GenomicRanges, IRanges, GenomeInfoDb, BSgenome, Biostrings, VariantAnnotation, googleAuthR, httr, jsonlite, methods, parallel, rtracklayer, RCurl Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, seqminer, Rsamtools, MatrixGenerics, badger License: Artistic-2.0 MD5sum: 3122cb61fe1e32c6b211dfe2629f2027 NeedsCompilation: no Package: muscat Version: 1.10.1 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, 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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: a11e4d15df00f24e0fcf7d1b2eb26806 NeedsCompilation: no Package: MVCClass Version: 1.70.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: d1cb7a63cd00e8025d4e023e70fbff9d NeedsCompilation: no Package: MWASTools Version: 1.20.0 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: 7a53825f711c7576fca420dbbc3704f4 NeedsCompilation: no Package: mygene Version: 1.32.0 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: 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Package: netboost Version: 2.4.1 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: 37e6f3e4f065db1c1c41bd65e7c94fd8 NeedsCompilation: yes Package: netboxr Version: 1.7.1 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: 36a728b7f86124efe44b3e756c702173 NeedsCompilation: no Package: netDx Version: 1.8.0 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, 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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: 7f37a033357b620ee16ed1a0f1098452 NeedsCompilation: no Package: netSmooth Version: 1.16.0 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: 7fac3e4e0e31890d851ada7212582f7c NeedsCompilation: no Package: networkBMA Version: 2.35.0 Depends: R (>= 2.15.0), stats, utils, BMA, Rcpp (>= 0.10.3), RcppArmadillo (>= 0.3.810.2), RcppEigen (>= 0.3.1.2.1), leaps LinkingTo: Rcpp, RcppArmadillo, RcppEigen, BH License: GPL (>= 2) 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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: b683659286fc7a570fd89c9799ef3055 NeedsCompilation: no Package: normalize450K Version: 1.24.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 2739c9e1439a4fc48ecf183465fc71bf NeedsCompilation: no Package: NormalyzerDE Version: 1.14.0 Depends: R (>= 3.6) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, Biobase, RcmdrMisc, raster, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: 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NeedsCompilation: no Package: npGSEA Version: 1.32.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: 02d9c6eef849c5b5f6023b500a291f2d NeedsCompilation: no Package: NTW Version: 1.46.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 MD5sum: a6b4982d2c52ab8aabde69cf86400308 NeedsCompilation: no Package: nucleoSim Version: 1.24.0 Imports: stats, IRanges, S4Vectors, graphics, methods Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 8842d3d7c109d3b9efe7ae9e00e82394 NeedsCompilation: no Package: nucleR Version: 2.28.0 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) 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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: 3d97b955958a9003303cb643b065f620 NeedsCompilation: yes Package: occugene Version: 1.56.0 Depends: R (>= 2.0.0) License: GPL (>= 2) MD5sum: 0137d41a15935d85d68d6f289a93fd6a NeedsCompilation: no Package: OCplus Version: 1.70.0 Depends: R (>= 2.1.0) Imports: multtest (>= 1.7.3), graphics, grDevices, stats, akima License: LGPL MD5sum: dfec6d9711f126a36782eb2504569ace NeedsCompilation: no Package: ODER Version: 1.2.0 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: b70000b3486b0137221f407db7d2f478 NeedsCompilation: no Package: odseq Version: 1.24.0 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: ca7c77b5686d347a6efc955cf31f80f4 NeedsCompilation: no Package: OGRE Version: 1.0.0 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 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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: d6d0c07e3ff0ac3d47149a36ee873730 NeedsCompilation: no Package: OmicsLonDA Version: 1.12.0 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: 6178c8b6b26c902aac79b1daba047783 NeedsCompilation: no Package: OMICsPCA Version: 1.14.0 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: bb41d23653bff2fb6f1dc80f4cf8170a NeedsCompilation: no Package: omicsPrint Version: 1.16.0 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: 3f29990f2d4c1328ba535a620d5db129 NeedsCompilation: no Package: omicsViewer Version: 1.0.1 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: 3c005e6242121d733bf4a07656d2846c NeedsCompilation: no Package: Omixer Version: 1.6.0 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: 69bb21625776bb9abce95edd2ef04a2b NeedsCompilation: no Package: OmnipathR Version: 3.4.7 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, stats, stringr, tibble, tidyr, tidyselect, tools, utils, withr, xml2, yaml Suggests: BiocStyle, bookdown, dnet, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, rmarkdown, smoof, supraHex, testthat License: MIT + file LICENSE MD5sum: 947925b322a42fb51763a0787812deed NeedsCompilation: no Package: ompBAM Version: 1.0.0 Imports: utils, Rcpp, zlibbioc Suggests: RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 4485a52ce72047a7d04fc9973cfef5fe NeedsCompilation: no Package: oncomix Version: 1.18.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: f88bca5e079ccf3dda3adfe0f48f9188 NeedsCompilation: no Package: OncoScore Version: 1.24.0 Depends: R (>= 4.1.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: bc524c8f64b7d41e2b0a7a501bcec5ce NeedsCompilation: no Package: OncoSimulR Version: 3.4.0 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: cc391e9e45ca4b1959bd21a58686c037 NeedsCompilation: yes Package: oneSENSE Version: 1.18.0 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: 35ec588a867c52885c0b8ef3e4d4a0c6 NeedsCompilation: no Package: onlineFDR Version: 2.4.0 Imports: stats, Rcpp, RcppProgress, dplyr, tidyr, ggplot2, progress LinkingTo: Rcpp, RcppProgress Suggests: knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: effd4226e6941e79322a28d614ee4b50 NeedsCompilation: yes Package: ontoProc Version: 1.18.0 Depends: R (>= 3.5), ontologyIndex Imports: Biobase, S4Vectors, methods, AnnotationDbi, stats, utils, BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph, AnnotationHub Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown License: Artistic-2.0 MD5sum: bc7e208544d558ff11182a2122d16fb4 NeedsCompilation: no Package: openCyto Version: 2.8.4 Depends: R (>= 3.5.0) Imports: methods,Biobase,BiocGenerics,gtools,flowCore(>= 1.99.17),flowViz,ncdfFlow(>= 2.11.34),flowWorkspace(>= 3.99.1),flowStats(>= 3.99.1),flowClust(>= 3.11.4),MASS,clue,plyr,RBGL,graph,data.table,ks,RColorBrewer,lattice,rrcov,R.utils LinkingTo: Rcpp Suggests: flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML License: file LICENSE MD5sum: 676ba598f0d412d4210d3288cdd6048c NeedsCompilation: yes Package: openPrimeR Version: 1.18.0 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 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Version: 1.24.0 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: 77a3f38d1d882756270ca660d2533efe NeedsCompilation: no Package: OrganismDbi Version: 1.38.1 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: d7676211728e7e82f0a78bf5dfbcc754 NeedsCompilation: no Package: 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methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, checkmate, boot, coop LinkingTo: Rcpp Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown License: Artistic-2.0 MD5sum: a8c9e953f324696fc605ba2cce6c2b19 NeedsCompilation: yes Package: phemd Version: 1.12.0 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: 17a39657b97580dd22f524f6fdca03f5 NeedsCompilation: no Package: PhenoGeneRanker Version: 1.4.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 International License MD5sum: 81636f9dd971ba3424332f608b988172 NeedsCompilation: no 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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: 3dcac32ff2b2aa182a5e04ccea5d7de8 NeedsCompilation: no Package: Rnits Version: 1.29.0 Depends: R (>= 3.6.0), Biobase, ggplot2, limma, methods Imports: affy, boot, impute, splines, graphics, qvalue, reshape2 Suggests: BiocStyle, knitr, GEOquery, stringr License: GPL-3 MD5sum: 24a71a594ac12748631a6437bef3d364 NeedsCompilation: no Package: roar Version: 1.32.0 Depends: R (>= 3.0.1) Imports: methods, BiocGenerics, S4Vectors, IRanges, 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TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle License: Artistic-2.0 | file LICENSE MD5sum: 0ae178e7e6673b879c99adeab5efcc1e NeedsCompilation: yes Package: rsbml Version: 2.54.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils Imports: BiocGenerics, graph, utils License: Artistic-2.0 MD5sum: 6359bc3b8d376cc370f8e0d7006aca3d NeedsCompilation: yes Package: rScudo Version: 1.12.0 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: 91e13f0c6d563fc7596603a114c75c19 NeedsCompilation: no Package: rsemmed Version: 1.6.0 Depends: R (>= 4.0), igraph Imports: methods, magrittr, stringr, dplyr Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 1205dff8cc97b2ac3c0d64f709a5546e NeedsCompilation: no Package: 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(>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: 07fccc637dd0fdb2ea1856a8710ff9bd NeedsCompilation: no Package: ScaledMatrix Version: 1.4.1 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular License: GPL-3 MD5sum: 6418d59e8761f118adb603ccb086ceb8 NeedsCompilation: no Package: scAlign Version: 1.9.0 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: 19afbe5209347df6e169592d22c79bc2 NeedsCompilation: no Package: SCAN.UPC Version: 2.38.0 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: 4ade1c299159a07d3399e7c43fa58376 NeedsCompilation: no Package: scanMiR Version: 1.2.0 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: a3e782a40470e7da06ae590335f424de NeedsCompilation: no Package: scanMiRApp Version: 1.2.0 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: 110bf1772d2a80c2a5578a2c05d4828d NeedsCompilation: no Package: scAnnotatR Version: 1.2.0 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: 509e36dac7c02ce93963cbb1b16a1e62 NeedsCompilation: no Package: SCANVIS Version: 1.10.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file LICENSE MD5sum: 83f62567b3f91365849b1f6367abb8f1 NeedsCompilation: no Package: SCArray Version: 1.4.0 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: c20c53af516274f315e2e780a72a2c0b NeedsCompilation: yes Package: SCATE Version: 1.6.0 Depends: parallel, preprocessCore, 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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: e56ab44112e33d52dd2ca2591273f0b6 NeedsCompilation: no Package: scDblFinder Version: 1.10.0 Depends: R (>= 4.0) Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, SingleCellExperiment, 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: 2533ee32f3b147723fba53b8ecbc94a8 NeedsCompilation: no Package: scDD Version: 1.20.0 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: 138c051792fff51e66ee88b5f64270b9 NeedsCompilation: yes Package: scde Version: 2.24.0 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: 2db0219b4d57810222bf38e07e93ce2a NeedsCompilation: yes Package: scds Version: 1.12.0 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: 02718680669609c19361bad7a769bd8c NeedsCompilation: 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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: fb9c001b85d2a7145ec1a996ea2ddb10 NeedsCompilation: yes Package: schex Version: 1.10.0 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: bab0f5aff3038bd6c5ca68c21a3eef94 NeedsCompilation: no Package: scHOT Version: 1.8.0 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, 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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: 492f0f965f20879c0325c0e5157b9203 NeedsCompilation: no Package: scoreInvHap Version: 1.18.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: d11817959067eb17798a524df6ca5326 NeedsCompilation: no Package: scp Version: 1.6.0 Depends: R (>= 4.0), QFeatures (>= 1.3.5) Imports: methods, stats, utils, SingleCellExperiment, SummarizedExperiment, MultiAssayExperiment, MsCoreUtils, matrixStats, S4Vectors, dplyr, magrittr, rlang Suggests: testthat, knitr, BiocStyle, 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rtracklayer, hash, dplyr, GenomicRanges, magrittr, glue (>= 1.3.0), rlang, scater (>= 1.11.0) LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat Suggests: Rsubread, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: fe96630700191fe0217c32a5a20b1533 NeedsCompilation: yes Package: scran Version: 1.24.1 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: e46c2f772c4892ab9d8b1c65e959dc16 NeedsCompilation: yes Package: scReClassify Version: 1.2.0 Depends: R (>= 4.1) Imports: randomForest, e1071, stats, SummarizedExperiment, SingleCellExperiment, methods 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utils, knitr, S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor, methods, scales, msigdbr, schex, tibble, ggplot2, igraph Suggests: testthat License: Artistic-2.0 MD5sum: e87cfd405aa193128f6a7a51a45d0a9a NeedsCompilation: no Package: scTHI Version: 1.8.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown License: GPL-2 MD5sum: 61270f0628b7a2f5140424f3f6680b51 NeedsCompilation: no Package: scTreeViz Version: 1.2.0 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: 54c55eeffb5042b302ecd54d6772137f NeedsCompilation: no Package: scuttle Version: 1.6.3 Depends: SingleCellExperiment 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flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc License: MIT + file LICENSE MD5sum: b0bbbc4e6f6ed49fb16a209fd8fc1d09 NeedsCompilation: no Package: sincell Version: 1.28.0 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: b6e2e4e6a401338666b8bd2b132146c8 NeedsCompilation: yes Package: single Version: 1.0.0 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: ebac37bde82e33f93f833b81eaf85ea1 NeedsCompilation: no Package: SingleCellExperiment Version: 1.18.1 Depends: SummarizedExperiment Imports: methods, utils, 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QuasR Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, parallel, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0) License: GPL-3 MD5sum: fb1b09872a644522138cc51d1ad82dbc NeedsCompilation: no Package: SingleR Version: 1.10.0 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocNeighbors, BiocParallel, BiocSingular, stats, utils, Rcpp, beachmat, parallel LinkingTo: Rcpp, beachmat Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scater, scran, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 + file LICENSE MD5sum: 9134d8a90954f8f4f97d14c252bfda03 NeedsCompilation: yes Package: singscore Version: 1.16.0 Depends: R (>= 3.6) Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, 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(>= 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: 97b467cbce87215641e6dee9d322d7e8 NeedsCompilation: no Package: sparseDOSSA Version: 1.20.0 Imports: stats, utils, optparse, MASS, tmvtnorm (>= 1.4.10), MCMCpack Suggests: knitr, BiocStyle, BiocGenerics, rmarkdown License: MIT + file LICENSE MD5sum: 66444ddeee402530855100971a05149a NeedsCompilation: no Package: sparseMatrixStats Version: 1.8.0 Depends: 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testthat, knitr, markdown License: GPL-3 MD5sum: 944b0aab18b10417d39e5739159577a6 NeedsCompilation: no Package: tigre Version: 1.50.0 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: ed6755c01e0891bb20af6acdff89ed26 NeedsCompilation: yes Package: TileDBArray Version: 1.6.0 Depends: DelayedArray (>= 0.15.16) Imports: methods, Rcpp, tiledb, S4Vectors LinkingTo: Rcpp Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat License: MIT + file LICENSE MD5sum: 7111439406463bea3d9256c7e0bb9d93 NeedsCompilation: yes Package: tilingArray Version: 1.74.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 MD5sum: 579bad9a70bf35e568a87b62ca5a2a6a NeedsCompilation: yes Package: timecourse Version: 1.68.0 Depends: R 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methods, shiny, BiocFileCache, readr, tools Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: cdf59af41182ea3289e7347f98247b08 NeedsCompilation: no Package: topconfects Version: 1.12.0 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: b729236ffc91e2da4677131dedb465da NeedsCompilation: no Package: topdownr Version: 1.18.0 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 (>= 1.2.10), 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: 37a1f5a8ddf937190d3522ffe34bc8e2 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S4Vectors Imports: utils, rtracklayer, Matrix, matrixStats, stats, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi Suggests: knitr, rmarkdown,BiocStyle License: GPL-3 + file LICENSE MD5sum: 0bc391c13b75334139ae0e059f1f1326 NeedsCompilation: no Package: tricycle Version: 1.4.0 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: 630a5d33d1b5a8e5533711596163dbee NeedsCompilation: no Package: trigger Version: 1.42.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 MD5sum: 634b63c9963d3cf98fedbe82da880c0d NeedsCompilation: yes Package: trio Version: 3.34.0 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: f41bd4eb4bbf6b99d978023b89575631 NeedsCompilation: no Package: triplex Version: 1.36.0 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: bee626a6f0fe918be7a745bf3f014dd8 NeedsCompilation: yes Package: tripr Version: 1.2.0 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: e3a2a4d309b59ba20132f9107eb5b434 NeedsCompilation: no Package: tRNA Version: 1.14.0 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: 9075354cc5ae0bd8cf904d9817d1e286 NeedsCompilation: no Package: tRNAdbImport Version: 1.14.0 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: 801e90878abcdc52d6c39166d233e6d2 NeedsCompilation: no Package: tRNAscanImport Version: 1.16.0 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: ed86941f119e0cc2933448126d7d4522 NeedsCompilation: no Package: TRONCO Version: 2.28.0 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: 9879abb7edcf24503e9d99c211d02c63 NeedsCompilation: no Package: TSCAN Version: 1.34.0 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: 69936fe192a9d444ec10cbbd019d44a4 NeedsCompilation: no Package: tscR Version: 1.8.0 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: e5561fc2032a0afe11785b5ef9fea429 NeedsCompilation: yes Package: tspair Version: 1.53.0 Depends: R (>= 2.10), Biobase (>= 2.4.0) License: GPL-2 MD5sum: 2ae2033a88f85b75e2f72ffdc6be0956 NeedsCompilation: yes Package: ttgsea Version: 1.4.0 Depends: keras Imports: tm, text2vec, tokenizers, textstem, stopwords, data.table, purrr, DiagrammeR, stats Suggests: fgsea, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: 4a906f8eb647dbef7d98678c5c56dd6c NeedsCompilation: no Package: TTMap Version: 1.18.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 MD5sum: b0106a59a1a1ecb03cc8172e4b8f26ac NeedsCompilation: no Package: TurboNorm Version: 1.44.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata License: LGPL MD5sum: 897a0830aca17fbb9070c4fa7d1e0d91 NeedsCompilation: yes Package: TVTB Version: 1.22.0 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: 25c357e1c9f1c9ac0f4f8e80ef410592 NeedsCompilation: no Package: tweeDEseq Version: 1.42.0 Depends: R (>= 2.12.0) Imports: MASS, limma, edgeR, parallel, cqn Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) MD5sum: 36ec45aea0a7d8b0db78607e59681d91 NeedsCompilation: yes Package: twilight Version: 1.72.0 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: a077e6321b23737aadaa2ad67bb72a8b NeedsCompilation: yes Package: twoddpcr Version: 1.20.0 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: a26620cdda6ce4be6dbf01caf68ef992 NeedsCompilation: no Package: txcutr Version: 1.2.0 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: 5654e24651c78d3456507f60e5f0f0a5 NeedsCompilation: no Package: tximeta Version: 1.14.1 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: 6fd3c840deb671c43a09194f11ab222d NeedsCompilation: no Package: tximport Version: 1.24.0 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, fishpond License: GPL (>= 2) MD5sum: 9da276e7a5c1c7f6341eccba54d7a307 NeedsCompilation: no Package: TypeInfo Version: 1.62.0 Depends: methods Suggests: Biobase License: BSD_2_clause MD5sum: 2ad0a9f18a29f42126e1b75581ff1138 NeedsCompilation: no Package: UCell Version: 2.0.1 Depends: R(>= 4.1.0) Imports: methods, data.table(>= 1.13.6), Matrix, BiocParallel, SingleCellExperiment, SummarizedExperiment Suggests: Seurat, scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 1946194bef427c7030cb00aed30d54ff NeedsCompilation: no Package: Ularcirc Version: 1.14.0 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: 1caff462ed4918e36dcd129789d59849 NeedsCompilation: no Package: UMI4Cats Version: 1.6.0 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: c0ad8e42de3594c55ed5139ff9230432 NeedsCompilation: no Package: uncoverappLib Version: 1.6.0 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, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, processx, Rsamtools, GenomicRanges Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: 9e9bd922e42f70ebddf5a6300375d0fe NeedsCompilation: no Package: UNDO Version: 1.38.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 67c833fe4452f5f272f29c76b19211f6 NeedsCompilation: no Package: unifiedWMWqPCR Version: 1.32.0 Depends: methods Imports: BiocGenerics, stats, graphics, HTqPCR License: GPL (>= 2) MD5sum: b6041dadfb7ecdb18495c766c0598fdf NeedsCompilation: no Package: UniProt.ws Version: 2.36.5 Depends: methods, utils, RSQLite, BiocGenerics (>= 0.13.8) Imports: AnnotationDbi, BiocFileCache, cellxgenedp, jsonlite, httr, httpcache, progress Suggests: RUnit, BiocStyle, knitr License: Artistic License 2.0 MD5sum: 563175f4c6b42677bd0d1d15a14f0d27 NeedsCompilation: no Package: Uniquorn Version: 2.16.0 Depends: R (>= 3.5) Imports: stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation Suggests: testthat, knitr, rmarkdown, BiocGenerics, RUnit License: Artistic-2.0 MD5sum: 830ca43a4b7691eead1c32d5a81918c9 NeedsCompilation: no Package: universalmotif Version: 1.14.1 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: 3f64427edea896d8e9d2b47703e74bdb NeedsCompilation: yes Package: updateObject Version: 1.0.0 Depends: R (>= 4.2.0), methods, BiocGenerics, S4Vectors Imports: utils, digest Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 4107afb432e264898f37e350c752bf4e NeedsCompilation: no Package: uSORT Version: 1.22.0 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: a83d673991bf1ba48bfb8d5bc1fec24f NeedsCompilation: no Package: VAExprs Version: 1.2.1 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: b15ffa0d53f259abcbd7b76817be5e67 NeedsCompilation: no Package: VanillaICE Version: 1.58.0 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: 5e680c6f829c2ab5737f08a1b49444f6 NeedsCompilation: yes Package: VarCon Version: 1.4.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: c88eb053a1c79f95e91c4d7db4bcb2a5 NeedsCompilation: no Package: variancePartition Version: 1.26.0 Depends: R (>= 4.0.0), ggplot2, limma, BiocParallel Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix, iterators, foreach, doParallel, gplots, RhpcBLASctl, progress, reshape2, 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: 037769ef54f934f8813f64a76be58b62 NeedsCompilation: no Package: VariantAnnotation Version: 1.42.1 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 Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, 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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: 26e3b2084570c84b54a57055df59fc1c NeedsCompilation: yes Package: VariantTools Version: 1.38.0 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: 217497641fc29ec4a2f2e417e7c3bc1b NeedsCompilation: no Package: VaSP Version: 1.8.0 Depends: R (>= 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NeedsCompilation: no Package: VERSO Version: 1.6.0 Depends: R (>= 4.1.0) Imports: ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 9b45aadb1ca2a409292c27b4cb14db9b NeedsCompilation: no Package: vidger Version: 1.16.0 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: d97dd4b08bfa9cf2d1156385d9238f8f NeedsCompilation: no Package: viper Version: 1.30.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: 1f835da7c14e57cecbac18ed82bcfb08 NeedsCompilation: no Package: ViSEAGO Version: 1.10.0 Depends: R (>= 3.6) Imports: data.table, AnnotationDbi, AnnotationForge, biomaRt, dendextend, DiagrammeR, DT, dynamicTreeCut, fgsea, GOSemSim, ggplot2, GO.db, grDevices, 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TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown License: GPL-3 MD5sum: 95d3fdcf7d52654bde2998c700c6cdc6 NeedsCompilation: no Package: vsn Version: 3.64.0 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: 5c2b98cd8b77eb02bb26ebd091b12308 NeedsCompilation: yes Package: vtpnet Version: 0.36.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: 03f978e252562dc8e827f324e7748493 NeedsCompilation: no Package: vulcan Version: 1.18.0 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: 563d31842ea8bcbcee4eeab92e0d79e9 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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: ebd275899c8d8ab4d45f418a83785b90 NeedsCompilation: no Package: widgetTools Version: 1.74.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: a3b3a73c4c9766f441d6853bc741b256 NeedsCompilation: no Package: wiggleplotr Version: 1.20.0 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: 3ac0bfde16761afb4e1a68bc78527ead NeedsCompilation: no Package: wpm Version: 1.6.0 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