R (>= 2.10), cluster, survival, multtest
R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics
BiocGenerics (>= 0.15.10), BiocFileCache (>= 2.99.3)
R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel,
ellipse
R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods
R (>= 2.14.0), Biobase, binom, methods, stats
R (>= 4.4), BiocParallel, matter, ontologyIndex
R (>= 3.6.0), Biobase, IRanges, methods, GenomicRanges
R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML,
ggplot2, rmarkdown
methods, BiocGenerics, S4Vectors (>= 0.47.2), IRanges,
Biostrings
R (>= 3.5.0), methods, utils, stats, graphics, parallel,
GenomicRanges
R (>= 2.15.0), S4Vectors, IRanges, Seqinfo, GenomicRanges
R (>= 3.5.0), GenomicRanges (>= 1.61.1), SummarizedExperiment
(>= 1.39.1)
R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>=
0.53.3), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.47.6),
IRanges (>= 2.17.3), S4Arrays (>= 1.5.4), SparseArray (>=
1.7.5)
SparseArray (>= 1.5.15), DelayedArray (>= 0.31.6)
S4Vectors (>= 0.23.18), IRanges, GenomicRanges,
SummarizedExperiment (>= 1.1.6)
R (>= 4.3.0), variancePartition (>= 1.36.1),
SingleCellExperiment, ggplot2
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 (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>=
0.47.6), IRanges (>= 2.23.9), Seqinfo, GenomicRanges (>=
1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>=
2.77.2), Rsamtools (>= 2.25.1)
R (>= 4.0.0), stats, methods, graphics, GGally, network, sna,
scales, matrixStats
R (>= 4.5), methods, rhdf5, BiocGenerics, SparseArray
R (>= 2.11.0), cluster, Biobase, methods
R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.53.2),
S4Vectors (>= 0.47.6)
R (>= 4.2), limma, DEXSeq, satuRn (>= 1.7.0), sva, ggplot2 (>=
3.3.5), pfamAnalyzeR
R (>= 3.3.0), methods, stats, utils, graphics
R (>= 4.4), BiocParallel, Matrix, methods
R (>= 4.0.0), DESeq2, limma, locfit, splines
R (>= 4.1.0), MultiAssayExperiment, SingleCellExperiment,
SummarizedExperiment, TreeSummarizedExperiment (>= 1.99.3)
R (>= 2.10), methods, BiocGenerics, Biobase
R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods,
minet, mclust, reshape2
BiocGenerics, S4Vectors, IRanges, Biostrings (>= 2.71.5)
BiocGenerics, DelayedArray, R (>= 4.1.0)
R (>= 2.6.0), methods, utils, graph, grid
R (>= 3.5.0), methods, Seqinfo, GenomicRanges (>= 1.61.1),
Biostrings (>= 2.77.2)
R (>= 3.4.0), biclust, SummarizedExperiment
R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>=
0.45.2), S4Vectors (>= 0.47.6), IRanges
R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>=
0.53.2)
R (>= 3.6.0),SummarizedExperiment, methods, Rcpp
Biobase, grDevices, graphics, methods, stats, splines, utils
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
alabaster.schemas, methods, utils, S4Vectors, rhdf5 (>=
2.47.6), jsonlite, jsonvalidate, Rcpp
methods, BiocGenerics, S4Vectors, DelayedArray (>= 0.33.3),
S4Arrays, SparseArray (>= 1.5.22), rhdf5 (>= 2.47.1),
HDF5Array, Matrix, Rcpp
rmarkdown (>= 2.5), tools, methods, ggplot2 (>= 3.4.0),
GGally, dplyr, rjson, shiny, shinydashboard, DT, stats, utils,
tximport (>= 1.17.4), cowplot, rlang, Rcpp
bigparallelr, bigstatsr, checkmate, digest, dplyr, Matrix,
pbapply, S4Vectors, SingleCellExperiment, stats,
SummarizedExperiment, tidyr, withr
utils, methods, grDevices, RSQLite, BiocManager, BiocVersion,
curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr2,
yaml, dplyr, BiocBaseUtils
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
Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel,
foreach, methods, stats, graphics, ggplot2, DRIMSeq,
BiocParallel
Biobase, BiocGenerics, coda, cowplot, ggExtra, ggplot2,
graphics, grDevices, MASS, methods, Rcpp (>= 0.11.3),
S4Vectors, scran, scuttle, stats, stats4, SummarizedExperiment,
viridis, utils, Matrix (>= 1.5.0), matrixStats, assertthat,
reshape2, BiocParallel, posterior, hexbin
methods, glmGamPoi, scran, scuttle, stats, utils,
SingleCellExperiment, SummarizedExperiment, Rcpp (>= 0.12.0),
RcppParallel (>= 5.0.1), rstantools (>= 2.1.1)
Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix,
parallel, MASS, locfit, fitdistrplus, stats, methods, graphics,
grDevices, SingleCellExperiment, SummarizedExperiment,
BiocParallel, utils
methods, beachmat, HDF5Array, DelayedArray, Rcpp
methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics,
Matrix, Rcpp
futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp,
abind, stats, graphics, utils, methods, dixonTest, ids
BiocBaseUtils, BiocGenerics, BiocIO, curl, GenomicRanges,
IRanges, methods, Rsamtools, S4Vectors, Seqinfo, stats, utils,
XVector
stats, utils, futile.logger, parallel, snow, codetools
BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray,
BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat (>=
2.25.1)
R6, RSQLite, Rcpp, XML, chk, fscache (>= 1.0.2), jsonlite,
lgr, lifecycle, methods, openssl, plyr, progress, rappdirs,
sched (>= 1.0.1), sqlq, stats, stringr, tools, withr, yaml
ggplot2, graphics, Rcpp, SummarizedExperiment, animation,
rlang, biocViews, sessioninfo, BiocStyle
methods, utils, grDevices, stats, crayon
stats, methods, utils, cluster, Matrix, Rcpp, igraph,
S4Vectors, BiocParallel, BiocNeighbors
dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel,
crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs
gplots, methods, grDevices, stats, SummarizedExperiment
AnnotationDbi, AnnotationFilter, AnnotationHub, biomaRt,
BiocGenerics, Biostrings, BSgenome, dplyr, ensembldb,
GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, IRanges,
lifecycle, magrittr, Matrix, methods, plyranges, Rcpp,
S4Vectors, stats, stringr, tibble, tidyr, utils, zeallot
SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots,
grDevices, methods, stats, utils
doParallel, ggplot2, gplots, graphics, grid, gtable, knnmi,
MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats,
SummarizedExperiment
combinat, GenomeInfoDb, GenomicRanges, ggplot2, ggtree,
Matrix, matrixStats, methods, pheatmap, snpStats, S4Vectors,
utils, VariantAnnotation, vcfR
BiocGenerics (>= 0.31.6), coda, EBarrays, gaga, gtools,
Seqinfo, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer,
S4Vectors (>= 0.9.25), sqldf, survival, VGAM
stats, S4Vectors, utils, methods, Matrix,
SummarizedExperiment, SingleCellExperiment, Rtsne, graphics,
grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp, Rdpack
(>= 0.7)
Rcpp, sparseMatrixStats, stats, BiocParallel, irlba,
SingleCellExperiment, Matrix, SummarizedExperiment
rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp
(>= 0.11.0), ggplot2,grid,gridExtra,
png,base64enc,DT,rsvg,jsonlite,stringi
graphics, stats, utils, methods, survival
Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, coop,
slam, matrixStats, methods
blaster, future, future.apply, grDevices, igraph, methods,
Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>=
2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils,
posterior, visNetwork, dplyr, tidyr, ggplot2, ggforce, scales
BiocGenerics, Biobase, IRanges, Rsamtools, Seqinfo, S4Vectors
BiocParallel, cluster, methods, gplots, graphics, grDevices,
RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats,
SummarizedExperiment, tools, utils, rhdf5, dplyr, fgsea,
forcats, ggplot2
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, Rcpp, data.table, RColorBrewer, scales, grid, plyr,
knitr, abind, clue, grDevices, utils, pdist, magrittr,
reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach,
coda
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
Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods,
S4Vectors, IRanges, Seqinfo, stats, BiocParallel, metapod,
utils
viridis, methods, shiny, graphics, stats, grDevices, utils,
BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment,
flowCore, Biobase, Rcpp, BiocNeighbors
Rcpp, SummarizedExperiment, utils, methods, ComplexHeatmap,
circlize, ashr, data.table, BiocParallel, dplyr, stats,
magrittr, rlang, S4Vectors
cytolib(>= 2.3.10), flowCore (>= 1.99.10), flowWorkspace (>=
4.1.8), openCyto (>= 1.99.2), XML, data.table, jsonlite, RBGL,
Rgraphviz, Biobase, methods, graph, graphics, utils, jsonlite,
dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, stats,
tibble
methods, DBI, S4Vectors, IRanges, XVector
graphics, grDevices, methods, stats, utils
Rcpp, basilisk, assertthat, reticulate, Rtsne, irlba
BiocGenerics (>= 0.7.5), Biobase, BiocParallel, matrixStats,
methods, stats4, locfit, ggplot2 (>= 3.4.0), Rcpp (>= 0.11.0),
MatrixGenerics
methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel,
foreach, stats, BANDITS, Matrix, SingleCellExperiment,
SummarizedExperiment, ggplot2, tximport, gridExtra
grDevices, stats, methods, Matrix, MASS, checkmate, expm,
igraph, Rcpp, RcppArmadillo, RcppParallel, plyr, precrec
Rcpp, Biobase, stats, biwt, gtools, MASS, tools, dplyr,
methods, utils
dplyr, tidyr, numbers, purrr, stringr, stats, utils, methods,
Rcpp (>= 0.11.2), BH
edgeR, SummarizedExperiment, DelayedMatrixStats,
sparseMatrixStats, MatrixGenerics, Matrix, methods, purrr,
GSEABase, data.table, zenith (>= 1.1.2), mashr (>= 0.2.52),
ashr, dplyr, BiocParallel, ggbeeswarm, S4Vectors, IRanges,
irlba, limma, metafor, remaCor, broom, tidyr, rlang,
BiocGenerics, S4Arrays, SparseArray, DelayedArray, gtools,
reshape2, ggrepel, scattermore, Rcpp, lme4 (>= 1.1-33), MASS,
Rdpack, utils, stats
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
snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl,
digest, BiocGenerics, RcppAnnoy (>= 0.0.9)
matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize
(>= 0.4.5), IRanges
stats, methods, utils, data.table, BiocGenerics,
GenomicRanges, Rcpp
BiocParallel, data.table, matrixStats, stats, survival,
igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid,
bigmemory, graphics, utils
methods, graphics, grDevices, stats, utils
methods, graphics, grDevices, stats, BiocGenerics, S4Vectors,
IRanges
tcltk, graphics, grDevices, stats, utils
Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0),
cowplot, grid, fastmatch, Matrix, scales, utils
data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils
BiocGenerics, methods, Biobase, graph, flowCore, parallel
Biobase, BiocGenerics (>= 0.29.2), grDevices, graphics,
methods, stats, utils, stats4, Rcpp, matrixStats, cytolib (>=
2.13.1), S4Vectors
Biobase, BiocGenerics (>= 0.1.6), graphics, grDevices,
methods, stats, stats4
Biobase, BiocGenerics, cytolib (>= 2.13.1), XML, ggplot2,
graph, graphics, grDevices, methods, stats, stats4, utils,
RBGL, tools, Rgraphviz, data.table, dplyr, scales(>= 1.3.0),
matrixStats, RProtoBufLib, flowCore(>= 2.1.1), ncdfFlow(>=
2.25.4), DelayedArray, S4Vectors
RUnit, methods, ChemmineR, BiocGenerics, parallel
stats, utils, methods, ggplot2, tidyr, expm, Rcpp,
RcppParallel, gdsfmt
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
plyr, graph, htmlwidgets, Rgraphviz, RCy3, rjson, XML,
methods, grDevices, stats, graphics
methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, Biostrings, Rsamtools, BiocParallel, cigarillo
(>= 0.99.2)
methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges
(>= 2.19.13), data.table, stats4, stats, utils
Rcpp, RcppParallel, cli, dplyr, ggfun (>= 0.1.5), ggplot2,
grDevices, grid, methods, rlang, scattermore, stats, Seurat,
SingleCellExperiment, SummarizedExperiment, tidydr, tidyr,
tibble, utils, RColorBrewer, yulab.utils, scales
Rcpp, beachmat, DelayedMatrixStats, matrixStats,
MatrixGenerics, SparseArray (>= 1.5.21), S4Vectors,
DelayedArray, HDF5Array, Matrix, SummarizedExperiment,
SingleCellExperiment, BiocGenerics, methods, stats, utils,
splines, rlang, vctrs
Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0),
GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils,
grDevices, graphics, stats,
AnnotationDbi, dendextend, doParallel, foreach, parallel,
org.Hs.eg.db, GO.db, Rcpp, stats, graphics,
MultiAssayExperiment, IRanges, S4Vectors
AnnotationDbi, DBI, digest, GO.db, methods, rlang, R.utils,
stats, utils, yulab.utils (>= 0.2.1)
parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS,
stats, utils, grDevices
Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats
graphics, grDevices, reshape2, stats, utils
stats, tools, rhdf5filters, S4Vectors, IRanges, S4Arrays
rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>=
2.13.1), methods, GenomicRanges, abind, BiocParallel,
BatchJobs, h5vcData, GenomeInfoDb
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
data.table, InteractionSet, GenomicRanges,
SummarizedExperiment, Rcpp (>= 1.0.12), S4Vectors, gtools,
pbapply, BiocGenerics, Seqinfo
methods, utils, png, grDevices, circlize (>= 0.3.3), IRanges,
GenomicRanges, polylabelr, Rcpp
graphics, grDevices, stats, utils, BiocGenerics
Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges
methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel
(>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0),
SummarizedExperiment, tidyr
Rcpp, stats, splines, methods, utils, DESeq2,
SummarizedExperiment, fdrtool, genefilter, qvalue, Biobase,
BiocGenerics, BiocParallel, dplyr, grid, ggplot2, cowplot
hash, httr, Matrix, matrixStats, methods, Rcpp, rvest,
SingleCellExperiment, stats, stringr, utils
methods, stats, graphics, grid, lattice, grDevices
methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.27.12),
IRanges, Seqinfo
Rcpp, Matrix, data.table, methods, pbapply, parallelly,
stringfish,
methods, Rcpp, data.table, glue, stats, doParallel, parallel,
doRNG, foreach, iterators, ggplot2, HDInterval,
SummarizedExperiment, S4Vectors
methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>=
2.50.0), IRanges, GenomicRanges, RColorBrewer, rtracklayer,
VennDiagram, DBI, grDevices, graphics, stats, utils, Seqinfo,
grid, tximport (>= 1.7.1), tximeta (>= 1.7.12), edgeR,
futile.logger, stringr, dplyr, magrittr, readr, tibble,
XVector, BiocGenerics, RCurl, Biobase, SummarizedExperiment,
tidyr, S4Vectors, BiocParallel, pwalign
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
BiocGenerics, ProtGenerics, digest, irlba, stats, stats4,
graphics, grDevices, parallel, utils
dplyr (>= 1.0), methods, mgcv, caret, S4Vectors, stats, utils,
rlang, graphics, matrixStats, tidyr
ABSSeq, Biobase, BiocGenerics, BiocParallel, biomaRt,
Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter,
Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicFeatures,
GenomicRanges, gplots, graphics, grDevices, harmonicmeanp,
heatmaply, htmltools, httr, IRanges, jsonlite, lattice, log4r,
magrittr, MASS, Matrix, methods, NBPSeq, pander, parallel,
qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite, rtracklayer,
S4Vectors, stats, stringr, SummarizedExperiment, survcomp,
txdbmaker, utils, VennDiagram, vsn, yaml, zoo
Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats,
GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm,
data.table
ape, BiocGenerics, BiocParallel, Biostrings, bluster,
DECIPHER, decontam, DelayedArray, DelayedMatrixStats,
DirichletMultinomial, dplyr, IRanges, MASS, MatrixGenerics,
methods, rbiom, rlang, S4Vectors, scater, scuttle, stats,
stringr, tibble, tidyr, utils, vegan, Rcpp
BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>=
1.3-0), MatrixGenerics, S4Vectors, stats, stringr, methods,
igraph, irlba, utils, cowplot, BiocParallel, BiocSingular,
limma, ggplot2, tibble, matrixStats, ggraph, gtools,
SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel,
ggbeeswarm, RColorBrewer, grDevices, Rcpp, pracma, numDeriv
methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory,
foreach, ggplot2, parallel, parallelDist, reshape2, plyr,
biganalytics, stringr, Hmisc, utils
WGCNA, flashClust, dynamicTreeCut, GFA, igraph, RColorBrewer,
grid, MCL, fabia, NMF, biclust, iBBiG, BicARE, isa2, methods,
rJava, BiBitR, rqubic, Biobase, PMA, stats, dbscan, mclust,
SOMbrero, ppclust, Rcpp, utils, SummarizedExperiment, GSEABase,
org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE,
MatrixCorrelation, energy
corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler,
ReactomePA, DOSE, survival, grDevices, graphics, stats, utils,
Rcpp, RColorBrewer, grid, org.Hs.eg.db, foreach, doParallel
reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, Matrix,
graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods,
ggplot2
cluster, graph, Rgraphviz, flexclust, lattice, naturalsort,
snowfall, stats4, tsne, methods, graphics, stats, utils,
Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices,
e1071, ggplot2, wesanderson
rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods,
RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array,
grDevices, stats, magrittr, forcats, utils, corrplot,
DelayedArray, Rtsne, uwot, basilisk, stringi
parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>=
0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>=
2.0.0), matrixStats, Rtsne, MASS, reshape2, leidenbase (>=
0.1.9), limma, tibble, dplyr, pheatmap, stringr, proxy, slam,
viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0)
MASS, splines, lattice, IRanges, GenomicRanges,
GenomicAlignments, Rsamtools, Seqinfo, S4Vectors
Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust,
isa2, QUBIC, akmbiclust, RColorBrewer
Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome,
S4Vectors, SummarizedExperiment, GenomicRanges, IRanges,
Rsamtools, Seqinfo
Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
S4Vectors, tools
Rcpp, Biostrings, GenomicRanges, IRanges, ape, doParallel,
dplyr, foreach, methods, parallel, pwalign, rlang, seqinr,
stats, stringi, stringr, tibble, tidyr, utils
ProtGenerics (>= 1.35.3), MsCoreUtils, S4Vectors, IRanges,
rawrr (>= 1.17.2), utils, BiocParallel
MSstatsConvert, data.table, checkmate, MASS, htmltools, limma,
lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel,
gplots, plotly, marray, stats, grDevices, graphics, methods,
statmod, parallel, rlang
data.table, log4r, methods, checkmate, utils, stringi, Rcpp,
parallel
dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats,
MSstatsConvert, data.table, Biostrings, MSstatsPTM, Rcpp,
checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse,
scales, stats, plotly, htmltools
dplyr, gridExtra, stringr, stats, ggplot2, stringi, grDevices,
MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp,
Biostrings, checkmate, ggrepel, plotly, htmltools
graphics, grDevices, stats, methods, fields
BiocGenerics, S4Vectors, methods, SummarizedExperiment, Rcpp,
edgeR (>= 3.42.0), dplyr, Matrix, limma, tidyr, stats, GGally,
ggplot2, tidyselect (>= 1.2.0), tibble, rlang, grDevices, csaw,
rmarkdown, xfun, DT, ggrepel, IRanges, utils, DelayedArray,
tools
Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3),
ncdf4
glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust,
parallel, GSA, limma, multtest, ICSNP, glmnet, network,
ggplot2, grDevices, graphics, stats, utils
ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer
methods, stats, utils, grDevices, parallel, GenomeInfoDb,
GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2),
bamsignals (>= 1.4), rtracklayer (>= 1.32)
methods, Biobase, BiocGenerics, flowCore(>= 1.99.17), flowViz,
ncdfFlow(>= 2.11.34), flowWorkspace(>= 3.99.1), flowClust(>=
3.11.4), RBGL, graph, data.table, RColorBrewer, grDevices
stats, utils, methods, BiocParallel, SummarizedExperiment,
limma, fdrtool, Rcpp
Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr,
tibble, ggplot2, tidyr
benchmarkme, dplyr, edgeR, foreach, ggplot2, graphics,
lifecycle, magrittr, methods, parallel, purrr, Rcpp (>=
0.12.0), RcppParallel (>= 5.0.1), rlang, rstantools (>= 2.1.1),
stats, tibble, tidybayes, tidyr (>= 0.8.3.9000), utils
Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods
AnnotationDbi, AnnotationHub, BiocFileCache, cluster,
colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR,
fastICA, fastmatch, ggplot2, ggrepel, graphics, grDevices,
highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma,
pairsD3, plyr, purrr, Rcpp (>= 0.12.14), recount, Rfast,
R.utils, reshape2, shinyjs, stringr, stats,
SummarizedExperiment, survival, tools, utils, XML, xtable,
methods
Biostrings, graphics, gtools, methods, stats, utils, HMMcopy,
rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges,
limma, Seqinfo, BiocGenerics, grDevices, zoo, BiocParallel,
S4Vectors
methods, data.table, Seqinfo, GenomicRanges, IRanges,
BiocGenerics, S4Vectors, Rcpp
curl, jsonlite, methods, paws.storage, R.utils, utils
utils, Seqinfo, data.table, IRanges, GenomicRanges, parallel,
Rsamtools
Rcpp, stats, Biobase, methods, BiocParallel, lme4
utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25),
IRanges (>= 2.13.12), XVector (>= 0.19.7), bitops,
BiocParallel, stats
methods, stats, utils, Matrix, RcppParallel, SKAT,
CompQuadForm, survey
Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook,
rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods,
nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel
data.table, Rcpp, magrittr, plyr, stringr, utils, stats,
methods, ggplot2, pheatmap, RColorBrewer, rhdf5, readr,
parallel, grDevices
methods, Rcpp, beachmat (>= 2.25.1), DelayedArray,
BiocNeighbors (>= 1.99.0), Rigraphlib, parallel
Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS,
emdbook, magrittr, utils
methods, parallel, digest, S4Vectors, IRanges, GenomicRanges,
Seqinfo, Biostrings
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, fastmatch
Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2,
reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster,
statmod
methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats,
BiocParallel, BiocNeighbors, stats, utils, Rcpp, beachmat (>=
2.25.1)
magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0)
Rcpp, stats, Matrix, SpatialExperiment, SummarizedExperiment,
BiocParallel (>= 1.0)
utils, stats, matrixStats, IRanges, XVector
Rcpp, Matrix, matrixStats (>= 0.60.0), methods
ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork,
gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices,
stats, utils, graphics, doFuture, doRNG, future, foreach
methods, graph, RBGL, parallel, BiocGenerics
methods, BiocGenerics, XVector, stringr, stringi, crayon,
grDevices
stats, utils, graphics, ggplot2, BiocParallel
ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta, stats, graphics
Rcpp (>= 1.0.8), BiocParallel, GenomicRanges, rlang,
Biostrings, utils, methods, igraph, stats, grDevices,
RColorBrewer, pheatmap, ggplot2, ggnetwork, intergraph
graphics, grDevices, methods, ncdf4, stats, utils, assertthat
utils, igraph, methods, graphics, stats, BiocParallel
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),
stringr (>= 1.5.1), 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
methods, utils, stats, tools, BiocGenerics, S4Vectors, IRanges
cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib,
flowWorkspace
cpp11, BH(>= 1.81.0.0), cytolib, RProtoBufLib
Rcpp, RcppArmadillo, RcppProgress, RcppSpdlog, Rhtslib,
stringfish
IRanges, XVector, Biostrings, Rcpp, S4Vectors
Rhtslib (>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings
Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0)
Rcpp, assorthead (>= 1.3.10), beachmat, BiocNeighbors
Rcpp, beachmat, assorthead (>= 1.3.5), BiocNeighbors
R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles
tkWidgets (>= 1.19.0), affydata, widgetTools, hgu95av2cdf
BiocStyle, rmarkdown, knitr, testthat, digest, Matrix,
alabaster.matrix
testthat, knitr, BiocStyle, chihaya, BiocSingular,
ResidualMatrix
knitr, BiocStyle, testthat (>= 3.0.0), BiocManager
batchelor, BiocStyle, bluster, knitr, magick, matrixStats,
patchwork, RcppArmadillo, rmarkdown, scater, scran, Seurat,
splatter, testthat (>= 3.0.0), UpSetR
IRanges, Seqinfo, GenomeInfoDb, GenomicRanges,
VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr,
AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR,
Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment,
ExperimentHub, gdsfmt, rmarkdown, HubPub
DESeq2, airway, knitr, rmarkdown, testthat
ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi,
BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat
(>= 3.0.0)
BiocStyle, knitr, rmarkdown, testthat, roxygen2
testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, testthat, tximport, BiocStyle,
GenomicFeatures, Biostrings
BiocStyle, knitr, rmarkdown, testthat, scRNAseq, magick
knitr, rmarkdown, BiocStyle, devtools, testthat
testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix
testthat, BiocStyle, knitr, rmarkdown, rcmdcheck,
BiocParallel, HDF5Array, beachmat.hdf5
testthat, BiocStyle, knitr, rmarkdown, pander, seewave
tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr,
limma
BiocFileCache, BiocStyle, GenomicFeatures, GenomeInfoDbData,
knitr, httr2, rmarkdown, rvest, tinytest, txdbmaker,
TxDb.Hsapiens.UCSC.hg19.knownGene
BiocParallel, testthat, BiocStyle, knitr, rmarkdown
BiocGenerics, tools, foreach, BBmisc, doParallel,
GenomicRanges, RNAseqData.HNRNPC.bam.chr14,
TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle,
knitr, batchtools, data.table
testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, xml2
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
knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut,
scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans,
kohonen, apcluster, DirichletMultinomial, vegan, fastcluster
testthat, BiocStyle, knitr, rmarkdown, devtools
knitr, rmarkdown, testthat, BiocStyle, txdbmaker,
TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene,
BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86
BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat
(>= 3.1.6)
BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat,
VGAM
knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater,
mclust, testthat (>= 3.0.0), splatter
data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics,
RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL,
BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs,
png,rmarkdown, BiocManager,bibtex,codetools
BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix,
BiocStyle, testthat, rmarkdown, knitr
Rsamtools, GenomicAlignments, RNAseqData.HNRNPC.bam.chr14,
BSgenome.Hsapiens.UCSC.hg19, testthat, knitr, rmarkdown,
BiocStyle
BiocParallel, knitr, rmarkdown, testthat, CAMERA
BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork
testthat, knitr, rmarkdown, BiocStyle, SeuratObject,
BiocFileCache, xml2
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
flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny,
testthat, devtools, flowWorkspaceData, ggplot2, progress
hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit
AnnotationDbi, org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures,
GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager
ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet,
BiocStyle, flowStats
testthat, flowWorkspaceData , knitr, rmarkdown, parallel
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
uwot, testthat, knitr, rmarkdown, BiocStyle
testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer,
apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply,
airway, glmGamPoi, BiocManager
testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata,
BiocStyle, reshape2, utils
lattice, parallel, MASS, RColorBrewer, DT, knitr, rmarkdown,
BiocStyle
AnnotationHub, knitr, rmarkdown, testthat,
BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19,
caret
BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub,
RUnit, muscData, scater, scuttle
BiocStyle, digest, knitr, rmarkdown, shiny
arrow, 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
BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat
(>= 3.0.0)
testthat, knitr, rmarkdown, reactome.db, AnnotationDbi,
parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation,
Seurat
testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown,
openCyto, flowStats(>= 4.7.1)
Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat,
flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto,
gridExtra
testthat, flowWorkspaceData (>= 2.23.2), knitr, rmarkdown,
ggcyto, parallel, CytoML, openCyto
BiocStyle, knitr, knitcitations, knitrBootstrap,rmarkdown,
codetools
BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown
affydata, tools, splines, hgu95av2cdf, hgu95av2probe
parallel, digest, Matrix, crayon, RUnit, knitr, markdown,
rmarkdown, BiocGenerics
class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer,
BiocStyle, knitr
RUnit, BiocGenerics, RBGL, knitr, shiny, STRINGdb, BiocStyle,
magick, rmarkdown, org.Hs.eg.db
knitr, rmarkdown, foreach, doRNG, doParallel, Biobase,
SummarizedExperiment, testthat, methods, BiocStyle
ShortRead, rtracklayer, BSgenome, GenomicFeatures,
RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19,
DESeq2, edgeR, RUnit, knitr, BiocStyle
GenomeInfoDb, Biobase, AnnotationDbi, annotate, Biostrings
(>= 2.77.2), SummarizedExperiment (>= 1.39.1), Rsamtools,
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, GenomeInfoDb
aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph,
knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater,
scatterpie (>= 0.2.4), scuttle, shadowtext, sf, SeuratObject,
SpatialExperiment, STexampleData, testthat (>= 3.0.0), MASS
testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, MASS,
statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown,
BiocStyle, TENxPBMCData, muscData, scran, dplyr
Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat
knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat
AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr,
org.Hs.eg.db, prettydoc, readr, rmarkdown, testthat, tidyr,
tidyselect, ROCR
SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle,
knitr
BiocParallel, ExperimentHub, TENxBrainData, HDF5Array,
testthat, knitr, rmarkdown, BiocStyle
knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt,
BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown
HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit,
RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA,
affydata, minfiData, sva
BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray,
knitr, markdown, rmarkdown, Rsamtools
rhdf5, BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0)
knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0),
markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2,
ggforce, ggrepel, patchwork
testthat, RColorBrewer, wesanderson, scales, gridExtra,
BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp
RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2),
BiocStyle
BiocStyle, dplyr, ggraph, ggplot2, igraph, knitr, markdown,
Peptides, randomForest, rmarkdown, scRepertoire, spelling,
testthat, tidygraph, viridis
XVector, GenomicRanges, Rsamtools, GenomicAlignments,
GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset,
RUnit, BiocStyle
BiocFileCache, BiocStyle, bsseq, ggplot2, ggridges, knitr,
microbenchmark, rmarkdown, GenomicRanges, IRanges, Rsamtools,
SummarizedExperiment, S4Vectors, testthat (>= 3.0.0)
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
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
BiocStyle, BiocManager, BSgenome, knitr, RMySQL, RUnit
ade4, BiocStyle, biomformat, dada2, knitr, mediation, miaViz,
microbiomeDataSets, NMF, patchwork, philr, phyloseq, reldist,
rhdf5, rmarkdown, testthat, topicdoc, topicmodels, yaml
testthat, mvtnorm, scater, scran, covr, knitr, rmarkdown,
uwot, scuttle, BiocStyle, MouseGastrulationData,
MouseThymusAgeing, magick, RCurl, MASS, curl, scRNAseq,
graphics, sparseMatrixStats
knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM,
BiocStyle
knitr, testthat, Seurat, SeuratObject, ggpubr, foreach,
psych, MultiAssayExperiment, SummarizedExperiment,
SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown,
data.table, tidyverse, BiocStyle, Matrix, markdown
destiny, Hmisc, knitr, Seurat, scater, testthat
knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat
(>= 3.0.0)
knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc
Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign
rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle
BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr,
lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5),
testthat
testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD,
impute, norm, pcaMethods, vsn, Matrix, preprocessCore,
missForest
BiocStyle, knitr, rmarkdown, tinytest, covr, markdown,
mockery, kableExtra
BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight
knitr, rmarkdown, tinytest, covr, mockery, testthat (>=
3.0.0)
testthat (>= 3.0.0), BiocStyle, knitr, Biostrings, pwalign,
plotly, scattermore, BiocManager
msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19),
knitr, XML, rmarkdown
BiocStyle, testthat (>= 1.0), knitr, rmarkdown
flowWorkspaceData, knitr, rmarkdown, markdown, testthat,
utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2),
MASS
knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra,
grid, reshape2, scales
knitr, rmarkdown, forcats, testthat, BiocStyle,
SingleCellExperiment
BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2,
BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi
testthat, knitr, parallel, devtools, rmarkdown, gplots, covr,
car, rstudioapi, spelling
BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle,
knitr, rmarkdown, BiocManager, MASS
QUBICdata, qgraph, fields, knitr, rmarkdown
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
BiocStyle, covr, knitr, testthat (>= 3.0.0), withr
Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr
testthat, parallel, BiocStyle, knitr, rmarkdown
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
bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr,
ggplot2, mockery, BiocParallel
knitr, testthat, BiocStyle, DT, rmarkdown
BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.47.7)
BiocStyle, knitr, rmarkdown, tinytest, mockery
GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures,
VariantAnnotation, TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14,
BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr
knitr, rmarkdown, GEOquery, affy, airway, QUBIC
BiocParallel, SparseArray (>= 0.0.4), DelayedArray,
HDF5Array, testthat, knitr, rmarkdown, BiocStyle
IRanges, GenomicRanges, SummarizedExperiment, Matrix,
DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle,
knitr
parallel, markdown, rmarkdown, crayon, SNPRelate, RUnit,
knitr, ggmanh, BiocGenerics
BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db,
markdown, rmarkdown, RUnit
knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db,
rmarkdown
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM,
R.utils
testthat, knitr, rmarkdown, BiocStyle, MatrixGenerics,
sparseMatrixStats, Matrix, S4Vectors, SummarizedExperiment,
SingleCellExperiment, scRNAseq, igraph
BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown,
testthat
Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate,
crayon, knitr, markdown, rmarkdown, Rsamtools,
VariantAnnotation
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, biomaRt, stringr, monocle
testthat, knitr, rmarkdown, BiocStyle, BiocGenerics,
SingleCellExperiment, scuttle, scrapper (>= 1.3.14), scRNAseq,
ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex
parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS,
BiocGenerics
FNN, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
HDF5Array, ExperimentHub, testthat, knitr, rmarkdown,
BiocStyle
testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle
RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz
testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle
devtools, MutationalPatterns, RUnit, BiocManager,
BiocGenerics, BiocStyle, knitr, rmarkdown
Hmisc, clinfun, xtable, Biobase, BiocManager
rtracklayer, BiocStyle, ggtree, labdsv, covr, knitr,
rmarkdown, testthat (>= 3.0.0), xml2, networkD3
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