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
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 (>= 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
doParallel, foreach, parallel, iterators, data.table, stringr,
survival, arm, stats, utils, methods
R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2)
R (>= 4.1), SingleCellExperiment, BiocFileCache, data.table,
utils, S4Vectors
R (>= 4.3.0), AnnotationHub, ExperimentHub,
MultiAssayExperiment, SingleCellExperiment,
SummarizedExperiment
R (>= 4.2.0), ExperimentHub, AnnotationHub
SpatialExperiment (>= 1.3.3), R (>= 3.6)
R (>= 4.1), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0)
R (>= 4.1), SingleCellExperiment, BiocFileCache
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
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
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
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
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
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
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
knitr, testthat, BiocStyle, rcellminer, rmarkdown
RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr,
Biobase, GEOquery, biomaRt, survminer, survey, rmarkdown
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, ggplot2, hrbrthemes, knitr, readr, rmarkdown,
scater, usethis, utils
VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle