R (>= 2.10), cluster, survival, multtest
R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics
BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1)
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
R (>= 3.5.0), methods, utils, stats, graphics, parallel,
GenomicRanges
R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
R (>= 3.5.0), GenomicRanges, SummarizedExperiment
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)
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), 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 (>= 0.45.4)
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)
R (>= 4.1.0), DelayedArray, BiocGenerics
R (>= 2.6.0), methods, utils, graph, grid
methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8),
Biostrings (>= 2.47.6), R (>= 3.5.0)
R (>= 3.5), methods, GenomicRanges (>= 1.37.2)
R (>= 3.4.0), biclust, SummarizedExperiment
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)
BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>=
2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6)
R (>= 3.6.0),SummarizedExperiment, methods, Rcpp
Biobase, grDevices, graphics, methods, stats, splines, utils
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
utils, methods, grDevices, RSQLite, BiocManager, BiocVersion,
curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr,
yaml, dplyr
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
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
BeadDataPackR, limma, AnnotationDbi, stats4, reshape2,
GenomicRanges, IRanges, illuminaio, methods, ggplot2
futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp,
abind, stats, graphics, utils, methods, dixonTest, ids
stats, utils, futile.logger, parallel, snow, codetools
BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray,
BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat (>=
2.21.1)
BiocFileCache, R6, RCurl, RSQLite, Rcpp, XML, chk, git2r,
jsonlite, lgr, lifecycle, methods, openssl, plyr, progress,
rappdirs, 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
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
dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel,
crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs
gplots, methods, grDevices, stats, SummarizedExperiment
AnnotationDbi, AnnotationFilter, biomaRt, BiocGenerics,
Biostrings, BSgenome, dplyr, ensembldb, GenomeInfoDb,
GenomicFeatures, GenomicRanges, ggplot2, IRanges, 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,
GenomeInfoDb, 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, GenomeInfoDb,
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, GenomeInfoDb, 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
Biostrings, stats, GenomicRanges, IRanges, Rcpp, RcppRoll,
data.table, GenomeInfoDb, S4Vectors, ggplot2, cowplot,
progress, ggseqlogo, viridis, ggpointdensity
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
plyr, graph, htmlwidgets, Rgraphviz, RCy3, rjson, XML,
methods, grDevices, stats, graphics
methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, Biostrings, Rsamtools, BiocParallel
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,
parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS,
stats, utils, grDevices
Deriv, DescTools, digest, pryr, stringr, BiocGenerics
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, GenomeInfoDb
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, igraph, keras3, magrittr, matrixStats, methods,
Rcpp (>= 0.12.11), reticulate, rvest, SingleCellExperiment,
stats, stringi, stringr, tensorflow, utils
methods, stats, graphics, grid, lattice, grDevices
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, BSgenome, plyr, reshape2, gridExtra, Biostrings (>=
2.50.0), IRanges, GenomicRanges, RColorBrewer, rtracklayer,
VennDiagram, DBI, grDevices, graphics, stats, utils,
GenomeInfoDb, 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
dplyr, ggplot2, KEGGREST, methods, Rcpp (>= 0.12.0),
RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>=
2.4.0), S4Vectors, stringr, SummarizedExperiment, tidyr,
dynamicTreeCut, dendextend
ABSSeq, Biobase, BiocGenerics, BiocParallel, biomaRt,
Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter,
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, linkcomm, MCL,
fabia, NMF, biclust, iBBiG, BicARE, isa2, s4vd, BiBitR, rqubic,
Biobase, PMA, stats, dbscan, subspace, 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,
linkcomm, utils, Rcpp, org.Hs.eg.db, foreach, doParallel
reshape2, GenomicRanges, pheatmap, deepSNV, grDevices,
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, GenomeInfoDb, S4Vectors
Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust,
isa2, QUBIC, akmbiclust, RColorBrewer
Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome,
S4Vectors, SummarizedExperiment, GenomicRanges, IRanges,
Rsamtools, GenomeInfoDb
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 (>= 1.13.1), 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
dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats,
MSstatsConvert, data.table, Biostrings, MSstatsPTM, Rcpp,
checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse,
scales, stats
dplyr, gridExtra, stringr, stats, ggplot2, stringi, grDevices,
MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp,
Biostrings, checkmate, ggrepel
graphics, grDevices, stats, methods, fields
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)
affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1),
ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>=
1.0.0), splines, stats, stats4, utils, bit
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
lattice, grDevices, cowplot, methods, reshape2, stats, Matrix,
DelayedMatrixStats, DelayedArray, BiocSingular, BiocParallel,
Rcpp, dqrng
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
magrittr, ggplot2, dplyr, seqTools, zlibbioc, data.table,
reshape2, grDevices, graphics, stats, utils, Rcpp, rlang
Biostrings, graphics, gtools, methods, stats, utils, HMMcopy,
rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges,
limma, GenomeInfoDb, BiocGenerics, grDevices, zoo,
BiocParallel, S4Vectors
methods, data.table, GenomeInfoDb, GenomicRanges, IRanges,
BiocGenerics, S4Vectors, Rcpp
jsonlite, httr, stringr, R.utils, utils, paws.storage, methods
utils, GenomeInfoDb, data.table, IRanges, GenomicRanges,
parallel, Rsamtools
stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr,
scales
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, CompQuadForm,
survey
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
S4Vectors, utils, Matrix, SparseArray (>= 1.5.13),
BiocParallel, DelayedMatrixStats, SummarizedExperiment,
SingleCellExperiment, BiocSingular
Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0),EBSeq,
BiocParallel, mclust, SingleCellExperiment, cluster, Oscope,
SummarizedExperiment, stats, methods
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
Biobase, SingleCellExperiment, SummarizedExperiment,
BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy,
utils, googleVis, ggplot2, methods, stats, e1071, randomForest,
Rcpp (>= 0.12.12)
methods, Rcpp (>= 1.0.0), RcppParallel (>= 5.0.1), rstan (>=
2.21.3), rstantools (>= 2.1.0), VGAM, data.table, MASS,
logitnorm, ggplot2, matrixStats, assertthat, viridis, coda,
BiocStyle, cowplot, stats, SummarizedExperiment,
SingleCellExperiment, Matrix, dplyr, S4Vectors
data.table, Rcpp, magrittr, plyr, stringr, utils, stats,
methods, ggplot2, pheatmap, RColorBrewer, rhdf5, readr,
parallel, grDevices
methods, Rcpp, beachmat (>= 2.21.6), DelayedArray,
BiocNeighbors (>= 1.99.0), Rigraphlib, parallel
assertthat, cubature, dplyr, evmix, ggalluvial, ggdendro,
ggraph, grDevices, igraph, iNEXT, plyr, quantreg, Rcpp,
reshape2, rjson, rlang, S4Vectors, SeuratObject,
SingleCellExperiment, stringr, stringdist,
SummarizedExperiment, tidygraph, truncdist, VGAM, purrr,
lifecycle, methods
Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS,
emdbook, magrittr, utils
methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors,
BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays,
MatrixGenerics, SparseArray, DelayedArray, beachmat
methods, parallel, digest, S4Vectors, IRanges, GenomicRanges,
GenomeInfoDb, Biostrings
Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12),
GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), pwalign,
hwriter, methods, lattice, latticeExtra,
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 (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2,
reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster,
statmod
methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats,
BiocParallel, BiocNeighbors, stats, utils, Rcpp, beachmat (>=
2.23.5)
magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0)
graphics, grDevices, stats, utils, BiocGenerics, zlibbioc
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
methods, Biostrings, S4Vectors, IRanges, utils, stats,
parallel, graphics, grDevices, RSQLite, DBI
graphics, grDevices, methods, ncdf4, stats, utils, assertthat
utils, igraph, methods, graphics, stats, BiocParallel
doParallel, dplyr, flowCore, foreach, ggplot2, ggraph, glmnet,
methods, parallel, purrr, readr, recipes, rlang, stringr,
survival, tidygraph, tidyr, tidyselect, yardstick, Rcpp,
tibble, stats, utils, RcppHNSW
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
BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix,
methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment,
stats, SummarizedExperiment, utils
Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics,
stats
matrixStats, limma, parallel, shiny, qvalue, grDevices, stats,
MultiAssayExperiment, graphics
Rcpp (>= 1.0.1), arm (>= 1.10-1), eva, BiocFileCache (>=
2.6.0), BiocParallel, SingleCellExperiment, parallel, methods,
stats
methods, utils, tools, BiocGenerics, S4Vectors, IRanges
cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib,
flowWorkspace
cpp11, BH(>= 1.81.0.0), cytolib, RProtoBufLib
IRanges, XVector, Biostrings, Rcpp, S4Vectors
Rhtslib (>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings
Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0)
S4Vectors, IRanges, XVector, Biostrings, Rhtslib
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
IRanges, GenomicRanges, GenomeInfoDb, 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
lumi, vsn, affy, hwriter, beadarrayExampleData,
illuminaHumanv3.db, gridExtra, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr
testthat, BiocStyle, knitr, rmarkdown, pander, seewave
tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr,
limma
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, covr, xml2
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, covr, lgr
roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr,
rmarkdown, covr, lgr
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
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
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
knitr, BiocStyle, rmarkdown, BiocManager,
BSgenome.Hsapiens.UCSC.hg19, DT, rtracklayer, testthat (>=
3.0.0), RBGL
BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown
affydata, tools, splines, hgu95av2cdf, hgu95av2probe
parallel, digest, Matrix, crayon, RUnit, knitr, markdown,
rmarkdown, BiocGenerics
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
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
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
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, ggraph, ggplot2, knitr, graph, markdown,
rmarkdown, scRepertoire, spelling, testthat, tidygraph, viridis
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, rmarkdown, BiocStyle, testthat (>= 3.0.0)
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)
msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19),
knitr, XML, rmarkdown
BiocStyle, testthat (>= 1.0), knitr, rmarkdown
BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2,
pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr,
pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma,
RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt,
AnnotationDbi, ACME, RCurl
flowWorkspaceData, knitr, rmarkdown, markdown, testthat,
utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2),
MASS
knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra,
grid, reshape2, scales
testthat, scran, BiocGenerics, knitr, Biobase, GEOquery,
hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2,
airway, org.Hs.eg.db, magrittr, rmarkdown
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, tinytest, mockery
Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr
testthat, parallel, BiocStyle, knitr, rmarkdown
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
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,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14,
BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr
BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1),
genefilter, limma, org.Hs.eg.db, hgu133plus2.db,
GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit
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, rmarkdown, mclust, scater, BiocStyle
BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown,
rmarkdown, rhdf5, HDF5Array
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
BiocManager, BiocStyle, circlize, knitr, rmarkdown, scales,
scater, Seurat, spelling, testthat (>= 3.0.0), vdiffr, withr
BiocStyle, knitr, scRNAseq, rmarkdown, testthat,
sparseMatrixStats, DelayedMatrixStats, scran
Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate,
crayon, knitr, markdown, rmarkdown, Rsamtools,
VariantAnnotation
testthat, parallel, knitr, rmarkdown, BiocStyle
BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi,
knitr
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, scRNAseq, ggplot2,
pheatmap, grDevices, gridExtra, viridis, celldex
parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS,
BiocGenerics
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
knitr, testthat (>= 3.0.0), gplots, htmltools, BiocParallel
Hmisc, clinfun, xtable, Biobase, BiocManager
BiocStyle, knitr, igraph, markdown, rmarkdown
ConsensusClusterPlus, Biobase, broom, covr, diffcyt, emdist,
FlowSOM, forcats, ggrepel, HDCytoData, knitr, markdown,
philentropy, rmarkdown, Rtsne, statmod, SummarizedExperiment,
testthat (>= 3.0.0), lmerTest, lme4, ggridges, spelling,
scattermore, preprocessCore, SingleCellExperiment, Seurat,
SeuratObject, embed, rsample, BiocGenerics
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
breakaway, covr, knitr, rmarkdown, testthat, BiocStyle
knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle,
clusterProfiler, httr
affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr,
testthat
knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown,
scater