R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp
R (>= 2.15), methods, VariantAnnotation (>= 1.15.15)
R (>= 2.13.0), Biobase, GGtools, GenomicRanges, hgfocus.db
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 (>= 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
R (>= 3.3.0), minfi (>= 1.21.2),
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
R (>= 3.3), minfi (>= 1.21.2),
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0),
hgu133a.db, annotate
R (>= 3.0), EBImage, imageHTS, SearchTrees, limma,
RColorBrewer, gplots, splots, ggplot2, geneplotter, ChemmineR,
reshape2, plyr
R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate
R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils
R (>= 3.4), SummarizedExperiment, ExperimentHub
R (>= 2.12.0), methods, fields, sparseLDA, RNAinteract
R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf ,
RColorBrewer , methods, grid
Homo.sapiens, geuvPack, MultiAssayExperiment (>= 1.3.14)
BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biobase
AnnotationDbi, BiocGenerics, methods, GenomicRanges,
GenomeInfoDb, IRanges, readr, rtracklayer, S4Vectors, utils
utils, tidyr, magrittr, methods, S4Vectors
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
utils, rtracklayer, GenomicFeatures (>= 1.3.15)
Rcpp, stats, splines, methods, utils, DESeq2,
SummarizedExperiment, fdrtool, genefilter, qvalue, Biobase,
BiocGenerics, BiocParallel, dplyr, grid, ggplot2, cowplot
igraph, HTSanalyzeR, PANR, RedeR, pvclust, MASS
Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors
R.utils, Biobase, rpx, biocViews, BiocInstaller,
interactiveDisplay, shiny
GenomicRanges, exomeCopy, stringr, IRanges, S4Vectors
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
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
BiocStyle, survival, xtable, sva, genefilter, logging
survival, RUnit, metafor, genefilter, logging, sva, xtable,
futile.logger, BiocStyle
BiocInstaller, devtools, roxygen2, testthat, covr, knitr,
rmarkdown, BiocCheck, BiocStyle, BiocParallel, readr, RISmed,
ggplot2, metagenomeSeq, phyloseq, ape
BiocStyle, knitr, readr, rmarkdown, testthat
devtools (>= 1.6), knitcitations (>= 1.0.1), knitr (>= 1.6),
knitrBootstrap (>= 0.9.0), RefManageR, rmarkdown (>= 0.3.3),
BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK,
RSVGTipsDevice, cgdsr, hwriter, xtable, beeswarm
limma, rtracklayer, GenomicRanges, Rsamtools,
VariantAnnotation, tools, BiocStyle, knitr, testthat
ExperimentHub (>= 0.99.6), knitr, BiocStyle
AnnotationHub, knitr, rmarkdown, igraph, survival, ANF,
stats, testthat
testthat, RColorBrewer, wesanderson, scales, gridExtra,
BiocStyle, knitr, rmarkdown, airway, pasilla, DESeq, locfdr,
tidyr
knitr, BiocStyle, DESeq2, DEXSeq, edgeR, JunctionSeq
Biobase, BiocStyle, SummarizedExperiment, knitr, rmarkdown
xcms (>= 1.43.3), CAMERA, Risa (>= 1.0.0), knitr, Heatplus,
pcaMethods, sp
Rsamtools, GenomicAlignments, GEOquery, SRAdb,
GenomicFeatures, BiocStyle
gplots, RColorBrewer, cluster, vegan, clustsig
knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, isobar,
MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData,
rTANDEM, synapter, synapterdata, IPPD, Rdisop, OrgMassSpecR,
BRAIN, rols, hpar, GO.db, org.Hs.eg.db, biomaRt, RColorBrewer,
ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata,
MSGFplus, MSGFgui, MSnID, msmsTests, msmsEDA, corrplot,
Heatplus, gplots, VennDiagram, genefilter
Rsamtools, ShortRead, BSgenome.Dmelanogaster.UCSC.dm3,
GenomicAlignments, biomaRt, genomeIntervals
DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod,
gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid,
gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap,
BiocStyle, knitr
RUnit, BiocStyle, knitr, rmarkdown, systemPipeR
VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle
erma, BiocStyle, knitr, rmarkdown, gQTLstats (>= 1.9.2),
doParallel, geuvPack, knitcitations, bibtex