R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp
R (>= 3.5.0), AnnotationHub, ExperimentHub (>= 1.7.0),
SingleCellExperiment
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 (>= 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
doParallel, foreach, parallel, iterators, data.table, stringr,
survival, arm, MASS, stats, utils, methods
R (>= 3.4), SummarizedExperiment, ExperimentHub
R (>= 2.12.0), methods, fields, sparseLDA, RNAinteract
R (>= 3.5), ExperimentHub, AnnotationHub
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
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, tibble, utils
Rcpp, stats, splines, methods, utils, DESeq2,
SummarizedExperiment, fdrtool, genefilter, qvalue, Biobase,
BiocGenerics, BiocParallel, dplyr, grid, ggplot2, cowplot
utils, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures,
VariantAnnotation, Homo.sapiens, MTseeker
igraph, HTSanalyzeR, PANR, RedeR, pvclust, MASS
Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors
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
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, readr, rmarkdown, TCGAutils, testthat
sessioninfo, 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
knitr, rmarkdown, BiocStyle, iSEE, scater,
SingleCellExperiment, SummarizedExperiment, plyr
knitr, rmarkdown, EpiDISH, 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), scater,
igraph, iSEE, testthat
Biobase, BiocCheck, BiocManager, 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, ggbio, latex2exp
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
knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer,
CAGEfightR
BiocStyle (>= 2.2.0), 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, 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, plotly,
gridExtra, dplyr, lubridate
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
RUnit, BiocStyle, knitr, rmarkdown, systemPipeR
knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran,
scater, iSEE, testthat
BiocStyle, knitr, readr, readxl, dplyr, caret, randomForest,
doMC, e1071, DT
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