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), SummarizedExperiment,
genefilter, quadprog, nlme, S4Vectors, graphics, stats, utils,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19, ExperimentHub
R (>= 3.6), minfi (>= 1.21.2), SummarizedExperiment,
IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1),
IlluminaHumanMethylationEPICanno.ilm10b4.hg19, ExperimentHub(>=
1.9.1), FlowSorted.Blood.EPIC, utils
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 (>= 4.1), SingleCellExperiment, cytomapper,
R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome
R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub
Biobase, AnnotationHub, ExperimentHub, SummarizedExperiment, R
(>= 3.6.0)
SummarizedExperiment, ExperimentHub, R (>= 3.6.0)
R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment,
MultiAssayExperiment
R (>= 3.5.0), minfi (>= 1.21.2),
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
R (>= 3.3), 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
R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2)
R (>= 4.1), SingleCellExperiment, BiocFileCache, data.table,
utils, S4Vectors
R (>= 4.1), ExperimentHub, AnnotationHub, rmarkdown
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
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
ExperimentHub, utils, magrittr, dplyr, tidyr, mclust, ggplot2,
purrr, reshape2, viridis, ggthemes, stats, methods
BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>=
0.99.6), AnnotationHub, DESeq2
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
ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors,
GenomicRanges, stats, IRanges, 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
utils, methods, BiocGenerics, S4Vectors, GenomicRanges,
SummarizedExperiment, ExperimentHub, AnnotationHub,
AnnotationDbi, ensembldb, GenomicFeatures
ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr,
R.utils, stats, rhdf5
AnnotationHub, BiocFileCache, BiocGenerics, ExperimentHub,
HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment,
SummarizedExperiment, Matrix, methods, utils
shiny, golem, ggplot2, cowplot, plotly, viridisLite,
shinyWidgets, Polychrome, 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
BiocGenerics, jsonlite, remotes, GenomicFeatures,
GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer
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
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
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, cgdsr,
hwriter, xtable, beeswarm
Biobase, BiocStyle, 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
knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown,
testthat (>= 3.0.0)
knitr, rmarkdown, BiocGenerics, sva, BiocManager
knitr, rmarkdown, EpiDISH, FlowSorted.CordBloodCombined.450k,
FlowSorted.Blood.450k(>= 1.0.1), FlowSorted.CordBlood.450k,
FlowSorted.CordBloodNorway.450k, testthat,
IlluminaHumanMethylation450kmanifest(>= 0.2.0),
IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1),
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
knitr, rmarkdown, testthat,
IlluminaHumanMethylation450kmanifest(>= 0.2.0),
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
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
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
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
testthat, xtable, rmarkdown, knitr, BiocStyle, markdown
testthat, knitr, BiocStyle, rmarkdown, markdown
BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC
BiocFileCache, BiocStyle, data.table, knitr, rmarkdown
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
org.Sc.sgd.db, ppiStats, rmarkdown, knitr, BiocStyle
knitr, rmarkdown, markdown, BiocStyle, preciseTAD
gplots, RColorBrewer, cluster, vegan, clustsig
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, isobar, 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)
scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown,
testthat
BiocStyle, knitr, rmarkdown, BiocFileCache, testthat,
rappdirs, tools
GenomicRanges, BiocGenerics, sesame, testthat, knitr
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, pryr
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