R (>= 2.10), cluster, survival, multtest
R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics
R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase, GO.db
R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods
R (>= 2.14.0), Biobase, binom, methods, stats
R (>= 2.10), methods, tools, stats, genefilter
R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>=
0.53.3), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2),
IRanges (>= 2.17.3), S4Arrays (>= 1.5.4), SparseArray (>=
1.7.5)
SparseArray (>= 1.5.15), DelayedArray (>= 0.31.6)
blockmodeling, gplots, testthat, R (>= 3.0.0)
R (>= 3.6.0), methods, grid, ComplexHeatmap (>= 2.11.0),
GenomicRanges
R (>= 2.8.0), Biobase, coda, EBarrays, mgcv
R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats,
utils
R (>= 2.11.0), cluster, Biobase, methods
R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.53.2),
S4Vectors (>= 0.45.4)
R (>= 3.3.0), methods, stats, utils, graphics
R (>= 2.10), methods, BiocGenerics, Biobase
BiocGenerics, S4Vectors, IRanges, Biostrings (>= 2.71.5)
R (>= 2.6.0), methods, utils, graph, grid
R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>=
0.45.2), S4Vectors, IRanges
R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>=
0.53.2)
Biobase, grDevices, graphics, methods, stats, splines, utils
bit, DNAcopy, tilingArray, waveslim, cluster, aCGH
AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db
(>= 1.8.1), graphics, grDevices, KEGGREST (>= 1.30.1), multtest
(>= 1.6.0), stats (>= 2.1.0)
affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods,
preprocessCore, stats, utils
emdbook, SummarizedExperiment, GenomicRanges, methods, stats,
utils, Rcpp
SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp
(>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize,
grid, grDevices, graphics
methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges,
GenomicRanges, zlibbioc
methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics,
Matrix, Rcpp
ggplot2, graphics, Rcpp, SummarizedExperiment, animation,
rlang, biocViews, sessioninfo, BiocStyle
methods, utils, grDevices, stats, crayon
assertthat, methods, MASS, doParallel, parallel, e1071, earth,
foreach, randomForest, stats, IRanges, S4Vectors, data.table,
graphics, truncnorm, mvtnorm, Rcpp (>= 0.12.14), matrixcalc,
magrittr, kernlab, ggplot2, cowplot, BiocStyle
gplots, methods, grDevices, stats, SummarizedExperiment
SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots,
grDevices, methods, stats, utils
grDevices, graphics, grid, stats, utils, ComplexHeatmap (>=
2.5.4), matrixStats (>= 1.2.0), GetoptLong, circlize (>=
0.4.7), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer,
cluster, skmeans, png, mclust, crayon, methods, xml2,
microbenchmark, httr, knitr (>= 1.4.0), markdown (>= 1.6),
digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr,
foreach, doParallel, doRNG, irlba
methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, utils,
lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats,
VGAM, parallel, graphics, limma, beanplot
methods, DBI, S4Vectors, IRanges, XVector
Rcpp, basilisk, assertthat, reticulate, Rtsne, irlba
Rcpp, Biobase, stats, biwt, gtools, MASS, tools, dplyr,
methods, utils
Biobase, cluster, graphics, grDevices, lattice, methods, stats
BiocGenerics (>= 0.7.1), graphics, grDevices, stats, abind,
tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils,
htmltools, htmlwidgets, RCurl
matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize
(>= 0.4.5), IRanges
stats, methods, utils, data.table, BiocGenerics,
GenomicRanges, Rcpp
methods, graphics, grDevices, stats, utils
methods, graphics, grDevices, stats, BiocGenerics, S4Vectors,
IRanges
tcltk, graphics, grDevices, stats, utils
Biostrings, stats, GenomicRanges, IRanges, Rcpp, RcppRoll,
data.table, GenomeInfoDb, S4Vectors, ggplot2, cowplot,
progress, ggseqlogo, viridis, ggpointdensity
Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector,
Biostrings (>= 2.11.32), splines, BiocManager
MatrixGenerics (>= 1.11.1), AnnotationDbi, annotate, Biobase,
graphics, methods, stats, survival, grDevices
methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges
(>= 2.19.13), data.table, stats4, stats, utils
annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM
Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0),
GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils,
grDevices, graphics, stats,
AnnotationDbi, DBI, digest, GO.db, methods, rlang, R.utils,
stats, utils, yulab.utils (>= 0.1.6)
parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS,
stats, utils, grDevices
Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel,
methods, matrixStats
Rcpp (>= 1.0.0), RcppEigen(>= 0.3.2.0), Matrix, RANN, ape,
dendextend, ggplot2, mclust, patchwork, dplyr, grDevices,
methods, stats
methods, utils, png, grDevices, circlize (>= 0.3.3), IRanges,
GenomicRanges, polylabelr, Rcpp
graphics, grDevices, stats, utils, BiocGenerics
Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges
methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.27.12),
IRanges, GenomeInfoDb
methods, Rcpp, data.table, glue, stats, doParallel, parallel,
doRNG, foreach, iterators, ggplot2, HDInterval,
SummarizedExperiment, S4Vectors
methods, stats, Rcpp (>= 0.11.2), Matrix (>= 1.5-0), XVector
(>= 0.7.3), S4Vectors (>= 0.27.3), e1071, LiblineaR, graphics,
grDevices, utils, apcluster
grDevices, graphics, stats, utils, methods, statmod
Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan,
mclust, apcluster, ggplot2, ellipse, limma, utils, statmod,
MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo,
stats, amap, Rtsne, gmodels
data.table, grDevices, methods, RColorBrewer, Rhtslib,
survival, DNAcopy, pheatmap
Rcpp, SummarizedExperiment, utils, methods, ggplot2, dplyr,
magrittr, rlang, S4Vectors
cluster, graph, Rgraphviz, flexclust, lattice, naturalsort,
snowfall, stats4, tsne, methods, graphics, stats, utils,
Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices,
e1071, ggplot2, wesanderson
graphics, grDevices, stats, methods, fields
Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods
methods, data.table, GenomeInfoDb, GenomicRanges, IRanges,
BiocGenerics, S4Vectors, Rcpp
stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr,
scales
graphics, stats, utils, methods, e1071, parallel, foreach,
doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR,
robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1),
SummarizedExperiment, SingleCellExperiment, BiocGenerics,
S4Vectors
parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy,
RSpectra
methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions,
igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize,
ComplexHeatmap, grDevices, stats, utils, shiny
Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase,
methods, rsvd, SingleCellExperiment, SummarizedExperiment,
stats
graphics, grDevices, stats, utils, BiocGenerics, zlibbioc
utils, stats, matrixStats, IRanges, XVector
Rcpp, Matrix, matrixStats (>= 0.60.0), methods
methods, graph, RBGL, parallel, BiocGenerics
ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta, stats, graphics
methods, Biostrings, S4Vectors, IRanges, utils, stats,
parallel, graphics, grDevices, RSQLite, DBI
graphics, grDevices, methods, ncdf4, stats, utils, assertthat
methods, AnnotationDbi, gplots, graphics, grDevices, stats,
utils, annotate, DBI, RSQLite
strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4
BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>=
0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0),
grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>=
1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils
Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn,
grDevices, graphics, stats, utils
Biobase, graphics, grDevices, splines, stats
methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp,
Biostrings, BiocGenerics, S4Vectors, rlang, grid,
MatrixGenerics
Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics,
stats
BiocGenerics, genefilter, graphics, grDevices, gtools,
methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta,
siggenes
methods, utils, tools, BiocGenerics, S4Vectors, IRanges
IRanges, XVector, Biostrings, Rcpp, S4Vectors
tkWidgets (>= 1.19.0), affydata, widgetTools, hgu95av2cdf
DESeq2, airway, knitr, rmarkdown, testthat
ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi,
BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat
(>= 3.0.0)
testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
testthat, BiocStyle, knitr, rmarkdown, rcmdcheck,
BiocParallel, HDF5Array, beachmat.hdf5
tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr,
limma
BiocParallel, testthat, BiocStyle, knitr, rmarkdown
testthat, knitr, rmarkdown, lattice, latticeExtra,
rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db,
ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer
graphics, pwalign, BSgenome (>= 1.13.14),
BSgenome.Celegans.UCSC.ce2 (>= 1.3.11),
BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),
BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,
hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy
(>= 1.41.3), affydata (>= 1.11.5), RUnit, BiocStyle, knitr,
testthat (>= 3.0.0), covr
genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen,
NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE,
AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree,
dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot,
flexclust, randomForest, e1071
hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit
BiocParallel, HDF5Array (>= 1.17.12), genefilter,
SummarizedExperiment, airway, lobstr, DelayedMatrixStats,
knitr, rmarkdown, BiocStyle, RUnit
testthat, knitr, BiocStyle, rmarkdown, Matrix
knitr, rmarkdown, BiocStyle, ggplot2, uwot, testthat
lattice, parallel, MASS, RColorBrewer, DT, knitr, rmarkdown,
BiocStyle
AnnotationHub, knitr, rmarkdown, testthat,
BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19,
caret
BiocStyle, digest, knitr, rmarkdown, shiny
jsonlite, knitr, Matrix, readr, rhdf5, SeuratObject, splines,
AnnotationDbi, Biobase, BiocStyle, org.Hs.eg.db,
SummarizedExperiment
knitr, tximportData, testthat (>= 3.0.0)
testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter,
RColorBrewer
GenomeInfoDb, SummarizedExperiment, VariantAnnotation, RUnit,
knitr, rmarkdown, ggplot2
knitr, BiocStyle, rmarkdown, BiocManager,
BSgenome.Hsapiens.UCSC.hg19, DT, rtracklayer, testthat (>=
3.0.0), RBGL
affydata, tools, splines, hgu95av2cdf, hgu95av2probe
class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer,
BiocStyle, knitr
Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>=
2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>=
1.13.53), GenomicAlignments, rtracklayer, BSgenome,
GenomicFeatures, txdbmaker, Gviz, VariantAnnotation,
AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph,
RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST,
hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
TxDb.Athaliana.BioMart.plantsmart22,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr,
rmarkdown, BiocStyle
testthat, knitr, BiocStyle, rmarkdown, covr,
GenomicAlignments, Biostrings
GO.db, golubEsets, hu6800.db, vsn, Rgraphviz
Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat
AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr,
org.Hs.eg.db, prettydoc, rappdirs, readr, rmarkdown, testthat,
tidyr, tidyselect, ROCR
SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle,
knitr
HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit,
RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA,
affydata, minfiData, sva
BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0),
markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown
RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2),
BiocStyle
XVector, GenomicRanges, Rsamtools, GenomicAlignments,
GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset,
RUnit, BiocStyle
knitr, ggplot2, testthat, BEDMatrix, genio
BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines,
affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio,
org.Hs.eg.db, vsn
BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer,
moments, testthat, matrixStats
berryFunctions, Biostrings, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr,
mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment,
rmarkdown, S4Vectors, curl
knitr, rmarkdown, BiocStyle, testthat, covr
biomaRt (>= 2.34.1), circlize (>= 0.4.11), STRINGdb (>=
2.2.0), httr (>= 1.2.1), IRanges (>= 2.8.2), S4Vectors (>=
0.12.2), knitr, testthat, readr, rmarkdown
signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench
knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>=
2.22.0), BiocStyle
knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM,
BiocStyle
knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc
testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD,
impute, norm, pcaMethods, vsn, Matrix, preprocessCore,
missForest
BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2,
BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi
RUnit, knitr, rmarkdown, ggplot2, gridExtra, annotatr, LOLA,
org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, parallel,
doParallel, foreach, doRNG, matrixStats, EnvStats, ExtDist,
gamlss, gamlss.dist
Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr
knitr, rmarkdown, RUnit, testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2,
corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl
testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra,
BiocManager, stringr, stringi, ggplot2, tibble, lipidr
knitr, testthat, BiocStyle, DT, rmarkdown
BiocParallel, SparseArray (>= 0.0.4), DelayedArray,
HDF5Array, testthat, knitr, rmarkdown, BiocStyle
IRanges, GenomicRanges, SummarizedExperiment, Matrix,
DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle,
knitr
BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db,
markdown, rmarkdown, RUnit
knitr, rmarkdown, mclust, scater, BiocStyle
testthat, parallel, knitr, rmarkdown, BiocStyle
BiocGenerics, BiocStyle, testthat, knitr, igraph
knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC,
AnnotationDbi, Matrix, DiagrammeR, ragg, png,
InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment,
AnnotationHub, jsonlite
BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat
HDF5Array, ExperimentHub, testthat, knitr, rmarkdown,
BiocStyle
testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle
RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz
Hmisc, clinfun, xtable, Biobase, BiocManager
BiocStyle, knitr, igraph, markdown, rmarkdown
drosgenome1.db, puma, lumi, BiocStyle, BiocManager
rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer
spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb,
testthat, BiocParallel, seqLogo, motifStack, dplyr, ape,
ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio
affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr,
testthat