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
Biobase, stats, lattice, impute, AnnotationHub, ExperimentHub,
R (>= 3.5.0)
R (>= 3.3.0), minfi (>= 1.21.2),
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
R (>= 3.3), minfi (>= 1.21.2),
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
R (>= 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)
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
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)
AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra,
knitr, magrittr, methods, readr, S4Vectors, tibble, utils
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, DT, AnnotationDbi, 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
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, tidyverse, 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
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
BiocStyle, knitr, rmarkdown, FlowSOM, Rtsne, ggplot2
Biobase, BiocCheck, BiocInstaller, BiocStyle, circlize, covr,
cowplot, curatedMetagenomicData, dendextend, devtools, ggplot2,
gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats,
testthat
testthat, RColorBrewer, wesanderson, scales, gridExtra,
BiocStyle, knitr, rmarkdown, airway, pasilla, DESeq, locfdr,
tidyr
knitr, BiocStyle, DESeq2, DEXSeq, edgeR, JunctionSeq
BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC
Biobase, BiocStyle, SummarizedExperiment, knitr, rmarkdown
xcms (>= 3.0.0), 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,
SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db,
e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable,
lattice, mzID, pRoloc, pRolocdata, MSGFplus, MSGFgui, MSnID,
msmsTests, msmsEDA, DEP, corrplot, beanplot, Heatplus, gplots,
VennDiagram, protViz, 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
BiocStyle, knitr, readr, readxl, dplyr, caret, randomForest,
doMC, e1071, DT
knitr, BiocStyle, snow, BiocFileCache, BiocParallel,
data.table
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