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
R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub
Biobase, stats, lattice, impute, AnnotationHub, ExperimentHub,
SummarizedExperiment, R (>= 3.6.0)
SummarizedExperiment, 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 (>= 4.0), 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 (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2)
R (>= 4.0), ExperimentHub, AnnotationHub, rmarkdown
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
utils, ExperimentHub, AnnotationHub, AnnotationDbi, S4Vectors,
DelayedArray, DelayedMatrixStats
BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biobase
AnnotationDbi, BiocGenerics, methods, GenomicRanges,
GenomeInfoDb, IRanges, readr, rtracklayer, S4Vectors, utils
magrittr, methods, S4Vectors, tidyr, utils
AnnotationHub, ExperimentHub, HDF5Array, methods, 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,
grDevices, graphics, stats
GenomicFeatures, Gviz, readxl, plyr, rtracklayer,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
ExperimentHub, utils, magrittr, dplyr, tidyr, mclust, ggplot2,
purrr, reshape2, viridis, ggthemes, stats, methods
BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>=
0.99.6), AnnotationHub, DESeq2
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
ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors,
GenomicRanges, stats, IRanges, utils
Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors
grid, gdata, MASS, genefilter, methods, fields, utils,
lattice, Biobase
utils, methods, BiocGenerics, S4Vectors, GenomicRanges,
SummarizedExperiment, ExperimentHub, AnnotationHub,
AnnotationDbi, ensembldb, GenomicFeatures
ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr,
R.utils, stats, signatureSearch, rhdf5
AnnotationHub, BiocFileCache, BiocGenerics, ExperimentHub,
HCAMatrixBrowser, HDF5Array, S4Vectors, SingleCellExperiment,
SpatialExperiment, SummarizedExperiment, Matrix, methods, 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, SpatialExperiment, BiocFileCache,
jsonlite, tibble, readbitmap
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
testthat, knitr, rmarkdown, BiocStyle, DT
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
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
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, knitr (>= 1.6), RefManageR, rmarkdown (>=
0.3.3), BiocStyle
BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK,
RSVGTipsDevice, cgdsr, hwriter, xtable, beeswarm
Biobase, BiocStyle, 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, BiocGenerics, sva, BiocManager
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, scuttle, 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
BiocFileCache, BiocStyle, data.table, knitr, rmarkdown
Biobase, BiocStyle, SummarizedExperiment, knitr, rmarkdown
knitr, rmarkdown, BiocStyle, roxygen2, seqinr, readr
BiocStyle, knitr, testthat, specL (>= 1.2)
xcms (>= 3.11.8), 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, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize,
ComplexHeatmap, apeglm, rlang, GenomicAlignments, Rsamtools
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, survey
AnnotationDbi, rpx (>= 1.16.1), DT, knitr, rmarkdown,
BiocStyle, mzR, xcms, msdata, isobar, MALDIquant (>= 1.12),
MALDIquantForeign, readBrukerFlexData, synapter, synapterdata,
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, 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, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0),
covr, here, BiocManager
RUnit, BiocStyle, knitr, rmarkdown, systemPipeR
knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran,
scater, iSEE, testthat
knitr, BiocStyle, snow, BiocFileCache, BiocParallel,
data.table
knitr, BiocStyle, snow, BiocFileCache, BiocParallel
testthat (>= 1.0.0), knitr, rmarkdown, covr, BiocStyle
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