R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp
R (>= 3.6.0), SummarizedExperiment, ExperimentHub
R (>= 2.15), methods, VariantAnnotation (>= 1.15.15)
R (>= 3.6), SummarizedExperiment, ExperimentHub
R (>= 3.0.0), XML, ggplot2, impute, Biobase, BiocStyle
R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db
R (>= 2.15.0), utils, Biobase, SummarizedExperiment, GGBase
(>= 3.31.1)
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 (>= 2.12.0), methods, Biobase (>= 2.5.5), GGBase, snpStats,
illuminaHumanv1.db, AnnotationDbi
R (>= 2.10), 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 (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome
Biobase, stats, lattice, impute, AnnotationHub, ExperimentHub,
SummarizedExperiment, R (>= 3.6.0)
Biobase, stats, lattice, impute, AnnotationHub, ExperimentHub,
R (>= 3.6.0)
R (>= 3.3.0), minfi (>= 1.21.2),
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
R (>= 3.3), minfi (>= 1.21.2),
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment
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 (>= 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 (>= 2.12.0), methods, fields, sparseLDA, RNAinteract
R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2)
R (>= 3.5), ExperimentHub, AnnotationHub
R (>= 3.6), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0)
R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf ,
RColorBrewer , methods, grid
Homo.sapiens, geuvPack, MultiAssayExperiment (>= 1.3.14)
beeswarm, Biobase, DESeq2, devtools, dplyr, ggdendro, ggplot2,
glmnet, graphics, grDevices, grid, gtable, ipflasso, methods,
RColorBrewer, reshape2, scales, stats, SummarizedExperiment,
survival, tibble
BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biobase
AnnotationDbi, BiocGenerics, methods, GenomicRanges,
GenomeInfoDb, IRanges, readr, rtracklayer, S4Vectors, utils
magrittr, methods, S4Vectors, tidyr, utils
AnnotationHub, ExperimentHub, HDF5Array, 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
GenomicFeatures, Gviz, readxl, plyr, rtracklayer,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
ExperimentHub, utils, magrittr, dplyr, tidyr, mclust, ggplot2,
purrr, reshape2, viridis, ggthemes, stats, methods
utils, rtracklayer, GenomicFeatures (>= 1.3.15)
AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra,
knitr, magrittr, methods, readr, S4Vectors, 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
GenomicRanges, GenomicAlignments, methods, S4Vectors,
parallel, IRanges
utils, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures,
VariantAnnotation, Homo.sapiens, MTseeker
Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors
methods, BiocGenerics, S4Vectors, GenomicRanges,
SummarizedExperiment, ExperimentHub
ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr,
R.utils, stats, signatureSearch, rhdf5
AnnotationHub, BiocFileCache, ExperimentHub, rappdirs, utils
GenomicRanges, exomeCopy, stringr, IRanges, S4Vectors
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
ggplot2, grid, gridExtra, deSolve, dplyr, locfit
GenomicFiles (>= 1.13.6), VariantAnnotation (>= 1.23.1),
gQTLBase, SummarizedExperiment, GenomicRanges, dsQTL,
GenomeInfoDb
Biostrings, GenomicRanges, illuminaHumanv1.db,
illuminaHumanv2.db, illuminaHumanv3.db
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
parallel, GGtools, TxDb.Hsapiens.UCSC.hg19.knownGene,
org.Hs.eg.db, illuminaHumanv1.db
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
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
ape, covr, BiocCheck, BiocManager, BiocParallel, BiocStyle,
devtools, ggplot2, knitr, metagenomeSeq, phyloseq, readr,
RISmed, rmarkdown, roxygen2, testthat
BiocStyle, knitr, RaggedExperiment, readr, rmarkdown,
TCGAutils, testthat
knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2,
readr, tibble, stringr, tidyr
sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6),
RefManageR, rmarkdown (>= 0.3.3), BiocStyle
BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK,
RSVGTipsDevice, cgdsr, hwriter, xtable, beeswarm
Biobase, BiocStyle, knitr, pheatmap, pkgdown, Seurat,
SingleCellExperiment, SummarizedExperiment, testthat (>=
2.1.0), tibble, tidyr, utils, viper
knitr, rmarkdown, BiocStyle, iSEE, scater,
SingleCellExperiment, SummarizedExperiment, plyr
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
AnnotationHub, knitr, rmarkdown, igraph, survival, ANF,
stats, testthat
knitr, rmarkdown, BiocStyle, scran (>= 1.11.4), BiocSingular,
scater, Rtsne, igraph, iSEE, testthat
BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM,
mclust, diffcyt
Biobase, BiocCheck, BiocManager, BiocStyle, circlize, covr,
cowplot, curatedMetagenomicData, dendextend, devtools, ggplot2,
gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats,
testthat
Biobase, BiocCheck, BiocManager, BiocStyle, cowplot,
devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2,
stats, testthat, tibble, UpSetR
testthat, RColorBrewer, wesanderson, scales, gridExtra,
BiocStyle, knitr, rmarkdown, airway, pasilla, DESeq, locfdr,
tidyr, ggbio, latex2exp
knitr, BiocStyle, DESeq2, DEXSeq, edgeR, JunctionSeq
BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC
Biobase, BiocStyle, SummarizedExperiment, knitr, rmarkdown
knitr, rmarkdown, BiocStyle, roxygen2, seqinr, readr
BiocStyle, knitr, testthat, specL (>= 1.2)
xcms (>= 3.0.0), CAMERA, Risa (>= 1.0.0), knitr, Heatplus,
pcaMethods, sp
BiocStyle, dplyr, DropletUtils, knitr, GEOquery, Matrix,
matrixStats, methods, muscat, rmarkdown, R.utils, readxl,
scater, scds, Seurat
knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer,
CAGEfightR
BiocStyle (>= 2.2), DT, ggplot2, knitr, rmarkdown, testthat,
specL, lattice, scales
Rsamtools, GenomicAlignments, GEOquery, SRAdb,
GenomicFeatures, BiocStyle
gplots, RColorBrewer, cluster, vegan, clustsig
RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr,
Biobase, GEOquery, biomaRt, survminer
AnnotationDbi, rpx, DT, knitr, rmarkdown, BiocStyle, mzR,
xcms, msdata, isobar, MALDIquant (>= 1.12), MALDIquantForeign,
readBrukerFlexData, synapter, synapterdata, IPPD, 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, rmarkdown, BiocStyle, GenomicRanges, sessioninfo,
testthat
BiocStyle, AnnotationHub, AnnotationDbi, GenomicFeatures,
knitr, rmarkdown, BiocFileCache, testthat
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
knitr, rmarkdown, BiocStyle, knitcitations, testthat (>=
2.1.0), covr, here, BiocManager
RUnit, BiocStyle, knitr, rmarkdown, systemPipeR
knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran,
scater, iSEE, testthat
BiocStyle, knitr, readr, readxl, dplyr, caret, randomForest,
doMC, e1071, DT, htmltab
knitr, BiocStyle, snow, BiocFileCache, BiocParallel,
data.table
knitr, BiocStyle, snow, BiocFileCache, BiocParallel
BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq,
SummarizedExperiment
VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle
erma, BiocStyle, knitr, rmarkdown, gQTLstats (>= 1.9.2),
doParallel, geuvPack, knitcitations, bibtex