R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp
R (>= 4.1), minfi(>= 1.36.0), ExperimentHub
R (>= 3.6.0), SummarizedExperiment, ExperimentHub
R (>= 3.5), genomeIntervals, randomForest
R (>= 3.6), SummarizedExperiment, ExperimentHub
R (>= 3.0.0), XML, ggplot2, impute, Biobase, BiocStyle
R (>= 4.1.0), SummarizedExperiment, TreeSummarizedExperiment
R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db
GenomicRanges (>= 1.5.42), ShortRead, rtracklayer
R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0)
R (>= 3.5), minfi(>= 1.21.2), ExperimentHub
R (>= 3.5), Biobase, GSEABase, hgu95a.db
R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5),
Biostrings
R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots,
limma, vcd, LSD,EBImage
R (>= 3.0.0), affy, Biobase, boot, clue, cluster, genefilter,
geneplotter, gplots, gtools, KEGGREST, MASS, mouse4302.db,
RColorBrewer, xtable
R (>= 4.3.0), SingleCellExperiment, SpatialExperiment,
cytomapper,
R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome
R (>= 4.2.0), EBImage, SpatialExperiment
R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub
Biobase, AnnotationHub, ExperimentHub, SummarizedExperiment, R
(>= 3.6.0)
SummarizedExperiment, ExperimentHub, R (>= 3.6.0)
R (>= 4.2), SummarizedExperiment, TreeSummarizedExperiment
R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment,
MultiAssayExperiment
R (>= 3.5.0), minfi (>= 1.21.2),
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
R (>= 3.5.0), minfi (>= 1.21.2),
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
R (>= 4.1), SingleCellExperiment, SummarizedExperiment,
SpatialExperiment
R (>= 3.6), ExperimentHub, SingleCellExperiment
R (>= 3.6), AnnotationHub (>= 2.15), ExperimentHub (>= 1.0),
Biostrings (>= 2.51), gplots (>= 3.0), protViz (>= 0.4),
ShortRead (>= 1.41)
R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0),
hgu133a.db, annotate
R (>= 4.1.0), ExperimentHub, GenomicRanges, InteractionSet
R (>= 4.1), SummarizedExperiment, ExperimentHub
R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate
R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils
R (>= 3.6), limma, edgeR, ReactomeGSA, Seurat
doParallel, foreach, parallel, iterators, data.table, stringr,
survival, arm, stats, utils, methods
R (>= 3.4), SummarizedExperiment, ExperimentHub, DelayedArray
(>= 0.21.2), HDF5Array (>= 1.23.2)
R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2)
R (>= 4.1), SingleCellExperiment, BiocFileCache, data.table,
utils, S4Vectors
R (>= 3.5.0), ExperimentHub, GenomicAlignments, GenomicRanges,
base
R (>= 4.3.0), AnnotationHub, ExperimentHub,
MultiAssayExperiment, SingleCellExperiment,
SummarizedExperiment
R (>= 4.2.0), ExperimentHub, AnnotationHub
R (>= 4.1), ExperimentHub, SummarizedExperiment
SpatialExperiment (>= 1.3.3), R (>= 3.6)
R (>= 4.1), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0)
R (>= 4.1), SingleCellExperiment, BiocFileCache
R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf ,
RColorBrewer , methods, grid
ExperimentHub, AnnotationHub, markdown, rmarkdown, EBImage,
magick, magrittr, filesstrings, animation, einsum
BiocFileCache, GenomicRanges, GenomeInfoDb, GEOquery, graph,
methods, utils
beeswarm, Biobase, DESeq2, devtools, dplyr, ggdendro, ggplot2,
glmnet, graphics, grDevices, grid, gtable, ipflasso, methods,
RColorBrewer, reshape2, scales, stats, SummarizedExperiment,
survival, tibble
utils, ExperimentHub, AnnotationHub, AnnotationDbi, S4Vectors,
DelayedArray, DelayedMatrixStats
AnnotationDbi, BiocGenerics, methods, GenomicRanges,
GenomeInfoDb, IRanges, readr, rtracklayer, S4Vectors, utils
AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, mia,
purrr, rlang, stringr, tibble, tidyr, tidyselect
AnnotationHub, ExperimentHub, MultiAssayExperiment, rlang,
stats
AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors,
stats, SummarizedExperiment, utils
affy, frma, frmaTools, hgu133plus2.db, hgu133plus2frmavecs,
sva, rgl, ConsensusClusterPlus, cluster, siggenes, ROCR, pamr,
survival, gplots, AnnotationDbi, Biobase
grid, TSP, limma, rhdf5, knitr, abind, gplots, igraph,
grDevices, graphics, stats
GenomicFeatures, Gviz, readxl, plyr, rtracklayer,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
BiocFileCache, S4Vectors, rjson, utils, tools
ExperimentHub, utils, magrittr, dplyr, tidyr, mclust, ggplot2,
purrr, reshape2, viridis, ggthemes, stats, methods
BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>=
0.99.6), AnnotationHub, DESeq2
genefilter, nlme, quadprog, graphics, stats, utils,
AnnotationHub, SummarizedExperiment, S4Vectors
SummarizedExperiment,
IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1),
IlluminaHumanMethylationEPICanno.ilm10b4.hg19, utils,
AnnotationHub
BiocFileCache, HiCExperiment, GenomicRanges, IRanges,
S4Vectors, utils, tools
RCurl, XML, ExperimentHub, BiocGenerics, Rsamtools
utils, rtracklayer, GenomicFeatures (>= 1.3.15)
ExperimentHub (>= 1.14.0), AnnotationHub, AnnotationFilter,
data.table, utils, BSgenome, GenomeInfoDb, GenomicFeatures,
GenomicRanges, ensembldb
AnnotationHub, ExperimentHub, S4Vectors, assertthat, dplyr,
kableExtra, knitr, magrittr, methods, readr, stringr, tibble,
utils
AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra,
knitr, magrittr, methods, readr, S4Vectors,
SummarizedExperiment, phyloseq, MultiAssayExperiment,
data.table
Rcpp, stats, splines, methods, utils, DESeq2,
SummarizedExperiment, fdrtool, genefilter, qvalue, Biobase,
BiocGenerics, BiocParallel, dplyr, grid, ggplot2, cowplot
methods, utils, ExperimentHub, S4Vectors, DelayedArray,
HDF5Array
GenomicRanges, GenomicAlignments, methods, S4Vectors,
parallel, IRanges
grDevices, AnnotationHub, BumpyMatrix, ExperimentHub,
S4Vectors, SingleCellExperiment, SummarizedExperiment
BiocFileCache, Biostrings, data.table, dplyr, ggplot2,
magrittr, Matrix, MultiAssayExperiment, qlcMatrix, R.utils,
Rbowtie2, readr, rlang, Rsamtools, S4Vectors, stringr,
SummarizedExperiment, taxize, tidyr, tools
ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors,
GenomicRanges, stats, IRanges, utils
BiocFileCache, tools, S4Vectors, ape, utils
methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape
methods, ExperimentHub, BiocGenerics, S4Vectors, BumpyMatrix
ExperimentHub, utils, GSEABase, org.Mm.eg.db, org.Hs.eg.db,
AnnotationDbi, methods, stats, AnnotationHub
Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors
grid, gdata, MASS, genefilter, methods, fields, utils,
lattice, Biobase
AzureStor, DelayedArray, GenomicRanges, HDF5Array, S4Vectors,
checkmate, methods, rhdf5
utils, methods, BiocGenerics, S4Vectors, GenomicRanges,
SummarizedExperiment, ExperimentHub (>= 2.3.4), AnnotationHub
(>= 3.3.6), AnnotationDbi, ensembldb, GenomicFeatures
utils, readr, stringr, GenomicRanges, S4Vectors, IRanges,
GenomeInfoDb
ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr,
R.utils, stats, rhdf5
AnnotationHub, BiocBaseUtils, BiocFileCache, ExperimentHub,
HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment,
SummarizedExperiment, Matrix, methods, utils
shiny, golem, ggplot2, cowplot, plotly, viridisLite,
shinyWidgets, sessioninfo, grid, grDevices, methods,
AnnotationHub, utils, png, scater, DT, ExperimentHub,
RColorBrewer, SummarizedExperiment, stats, graphics, S4Vectors,
IRanges, fields, benchmarkme, SingleCellExperiment,
BiocFileCache, jsonlite, tibble, rtracklayer, Matrix,
BiocGenerics, GenomicRanges, magick, paletteer, scuttle, edgeR,
limma, statmod
methods, Biostrings, BiocGenerics, jsonlite, remotes
ExperimentHub, SingleCellExperiment, HDF5Array,
SummarizedExperiment, gdata, AnnotationHub
ggplot2, grid, gridExtra, deSolve, dplyr, locfit
AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr,
purrr, rlang, stringr, tibble, tidyr
Biostrings, GenomicRanges, illuminaHumanv1.db,
illuminaHumanv2.db, illuminaHumanv3.db
rmarkdown, knitr, BiocStyle, testthat, SummarizedBenchmark,
dplyr, ggplot2, rlang
AnnotationDbi, AnnotationHub, BiocStyle, DEXSeq,
ExperimentHub, GenomicFeatures, S4Vectors, depmap, knitr,
rmarkdown
BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt,
broom, colorspace, cowplot, dendsort, doParallel, foreach,
forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin,
IHW, limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db,
pheatmap, piano, readxl, Rtsne, tidyr, xtable
minfi, MultiAssayExperiment, knitr, rmarkdown, rexposome
testthat, knitr, rmarkdown, BiocStyle, DT, ensembldb
BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat,
GO.db, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db,
org.Rn.eg.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Dmelanogaster.UCSC.dm6.ensGene,
TxDb.Drerio.UCSC.danRer10.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
clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr,
BiocStyle
knitr, rmarkdown, GenomicFeatures, ChIPseeker, AnnotationDbi,
S4Vectors, DESeq2, fastqcr, devtools, testthat, readr, dplyr,
tidyr, ggplot2
knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr,
dplyr, tidyr, ggplot2, S4Vectors
BiocStyle, survival, xtable, sva, genefilter, logging
survival, RUnit, metafor, genefilter, logging, sva, xtable,
futile.logger, BiocStyle
BiocStyle, DT, knitr, readr, rmarkdown, scater, testthat,
utils, uwot, vegan
BiocStyle, DT, dplyr, HGNChelper, knitr, methods, rmarkdown,
SummarizedExperiment, sva, testthat
BiocStyle, knitr, RaggedExperiment, readr, rmarkdown,
TCGAutils, testthat
knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2,
readr, tibble, stringr, tidyr
sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>=
0.3.3), BiocStyle
BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK, hwriter,
xtable, beeswarm
dplyr, testthat, methods, BiocStyle, knitr, rmarkdown
Biobase, BiocStyle, OmnipathR, viper, knitr, pheatmap,
pkgdown, rmarkdown, Seurat, SingleCellExperiment,
SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils
BiocStyle, knitr, rmarkdown, testthat, DropletUtils
knitr, rmarkdown, BiocStyle, iSEE, scater,
SingleCellExperiment, SummarizedExperiment, plyr
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
BiocStyle, knitr, dplyr, devtools, DT, rmarkdown
testthat (>= 3.0.0), stringr, plyr, prettydoc, BiocStyle,
Homo.sapiens, RColorBrewer, rmarkdown, BiocFileCache, knitr
rmarkdown, BiocStyle, knitr, ExperimentHub, minfi
affy, hgu95av2.db, hgu95av2cdf, vsn, knitr
knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown,
testthat (>= 3.0.0)
knitr, rmarkdown, BiocGenerics, sva, BiocManager
knitr,rmarkdown, FlowSorted.CordBlood.450k,
FlowSorted.Blood.450k(>= 1.0.1),
EpiDISH,FlowSorted.CordBloodNorway.450k, testthat,
IlluminaHumanMethylation450kmanifest(>= 0.2.0),
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1),
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
FlowSorted.Blood.EPIC, knitr, rmarkdown, testthat,
IlluminaHumanMethylation450kmanifest(>= 0.2.0),
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
rtracklayer, dplyr, testthat, methods, BiocStyle, knitr,
rmarkdown
limma, rtracklayer, GenomicRanges, Rsamtools,
VariantAnnotation, tools, BiocStyle, knitr, testthat
ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown,
SummarizedExperiment, SingleCellExperiment
ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown
ExperimentHub, BiocStyle, RefManageR, knitr, rmarkdown,
testthat, minfi, tibble, sessioninfo
BiocGenerics, BiocStyle, knitr, rmarkdown, Harman (>= 1.23.3)
AnnotationHub, knitr, rmarkdown, igraph, survival, ANF,
stats, testthat
knitr, rmarkdown, BiocStyle, scran (>= 1.11.4), BiocSingular,
scater, scuttle, Rtsne, igraph, iSEE, testthat
BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM,
mclust
RUnit, BiocGenerics, markdown, BiocStyle, knitr, rmarkdown
testthat, methods, BiocStyle, knitr, rmarkdown
Biobase, BiocCheck, BiocManager, BiocStyle, circlize,
cowplot, dendextend, devtools, ggplot2, gridExtra, haven,
phyloseq, rmarkdown, roxygen2, stats, testthat, tidyr
Biobase, BiocCheck, BiocManager, BiocStyle, cowplot,
devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2,
stats, testthat, tibble, UpSetR
testthat, RColorBrewer, wesanderson, scales, gridExtra,
BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp
BiocStyle, knitr, rmarkdown, markdown, testthat
LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat
knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0)
grid, ggplot2, ggpubr, knitr, rmarkdown, testthat, BiocStyle
testthat, xtable, rmarkdown, knitr, BiocStyle, markdown
testthat, knitr, BiocStyle, rmarkdown, markdown
BiocStyle, biomformat, knitr, lintr, plyr, rmarkdown,
Rsubread, spelling, sys, testthat, usethis
BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC
BiocFileCache, BiocStyle, data.table, knitr, rmarkdown
rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia,
ggplot2, tidyr, dplyr, magrittr, tibble, purrr
knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat
knitr, rmarkdown, BiocStyle, roxygen2, seqinr, readr
singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown,
testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma
BiocStyle, knitr, rmarkdown, testthat, specL (>= 1.2)
xcms (>= 3.13.8), CAMERA, Risa (>= 1.0.0), knitr, Heatplus,
pcaMethods, sp, rmarkdown
BiocStyle, dplyr, DropletUtils, knitr, GEOquery, Matrix,
matrixStats, methods, muscat, rmarkdown, R.utils, readxl,
scater, scds, Seurat
knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize,
ComplexHeatmap, apeglm, rlang, rmarkdown, GenomicAlignments,
Rsamtools
knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer,
CAGEfightR
BiocStyle (>= 2.2), DT, ggplot2, knitr, rmarkdown, testthat,
specL, lattice, scales
knitr, rmarkdown, BiocManager, GenomicFeatures, S4Vectors,
devtools, testthat
Rsamtools, GenomicAlignments, GEOquery, SRAdb,
GenomicFeatures, BiocStyle
knitr, rmarkdown, markdown, BiocStyle, preciseTAD
pRoloc (>= 1.13.8), testthat, SummarizedExperiment
knitr, testthat, BiocStyle, rcellminer, rmarkdown
RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr,
Biobase, GEOquery, biomaRt, survminer, survey, rmarkdown
AnnotationDbi, rpx (>= 2.0.3), DT, knitr, rmarkdown,
BiocStyle, mzR, xcms, msdata, MALDIquant (>= 1.12),
MALDIquantForeign, readBrukerFlexData, Rdisop, OrgMassSpecR,
SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db,
e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable,
lattice, mzID, pRoloc, pRolocdata, MSnID, msmsTests, msmsEDA,
DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram,
protViz, genefilter, plotly, gridExtra, dplyr, lubridate,
magick, cleaver
knitr, DT, rmarkdown, testthat, BiocStyle
knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo,
testthat
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
BiocGenerics, IRanges, Matrix, knitr, rmarkdown, rstudioapi,
testthat (>= 3.0.0), devtools, BiocStyle, ExperimentHubData
scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown,
testthat
BiocStyle, knitr, rmarkdown, BiocFileCache, testthat,
rappdirs, tools
BiocGenerics, sesame, testthat, knitr, rmarkdown
BiocStyle, knitr, rmarkdown, SpatialFeatureExperiment,
testthat (>= 3.0.0)
DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod,
gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid,
gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap,
BiocStyle, knitr, BiocParallel
BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown,
scater, scran, UpSetR, uwot
knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0),
covr, here, BiocManager, lobstr
GenomicFeatures, GenomicRanges, IRanges, Rsamtools,
ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown,
systemPipeR
knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran,
scater, iSEE, testthat
ggplot2, testthat, knitr, rmarkdown, iSEE, BiocStyle
BiocStyle, knitr, rmarkdown, testthat, tools
knitr, BiocStyle, snow, BiocFileCache, BiocParallel,
data.table, rmarkdown
rmarkdown, knitr, BiocStyle, snow, BiocFileCache,
BiocParallel
testthat (>= 1.0.0), knitr, rmarkdown, markdown, covr,
BiocStyle
BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq,
SummarizedExperiment
BiocStyle, ggplot2, hrbrthemes, knitr, readr, rmarkdown,
scater, usethis, utils
VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle