R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics
BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1)
blockmodeling, gplots, testthat, R (>= 3.0.0)
R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats,
utils
R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.39.2),
S4Vectors (>= 0.33.3)
R (>= 2.10), methods, BiocGenerics, Biobase
BiocGenerics, S4Vectors, IRanges, Biostrings (>= 2.71.5)
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 (>= 3.5.0), methods, GenomicRanges (>= 1.37.2)
R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>=
0.45.2), S4Vectors, IRanges
R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>=
0.37.0)
BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>=
2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6)
R (>= 4.3.0), methods, Matrix, BiocGenerics (>= 0.43.1),
MatrixGenerics (>= 1.11.1), S4Vectors, S4Arrays (>= 1.4.1)
R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>=
1.27.6), SummarizedExperiment (>= 1.5.3)
R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0),
MatrixGenerics, GenomeInfoDb (>= 1.15.2), GenomicRanges (>=
1.41.5), SummarizedExperiment (>= 1.19.5), Rsamtools (>=
2.19.1)
affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods,
preprocessCore, stats, utils, zlibbioc
alabaster.schemas, methods, utils, S4Vectors, rhdf5 (>=
2.47.6), jsonlite, jsonvalidate, Rcpp
methods, BiocGenerics, S4Vectors, DelayedArray (>= 0.27.2),
S4Arrays, SparseArray, rhdf5 (>= 2.47.1), HDF5Array, Matrix,
Rcpp
utils, methods, grDevices, RSQLite, BiocManager, BiocVersion,
curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr,
yaml, dplyr
emdbook, SummarizedExperiment, GenomicRanges, methods, stats,
utils, Rcpp
methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges,
GenomicRanges, zlibbioc
SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats,
methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix,
DelayedArray, DelayedMatrixStats, BiocParallel, scuttle,
ResidualMatrix, ScaledMatrix, beachmat
methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics,
Matrix, Rcpp
Rcpp, S4Vectors, BiocParallel, stats, methods, Matrix
stats, utils, futile.logger, parallel, snow, codetools
BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray,
BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat
methods, utils, grDevices, stats, crayon
grDevices, stats, scales, Hmisc, RColorBrewer, dichromat,
BiocGenerics, S4Vectors (>= 0.23.19), IRanges (>= 1.99.28),
GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21),
SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>=
1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>=
1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4),
ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlang
stats, methods, utils, cluster, Matrix, Rcpp, igraph,
S4Vectors, BiocParallel, BiocNeighbors
rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp
(>= 0.11.0), ggplot2,grid,gridExtra,
png,base64enc,DT,rsvg,jsonlite,stringi
IRanges, GenomeInfoDb, GenomicRanges, ggplot2, nabor,
BiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools,
S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats,
utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment,
RColorBrewer, BSgenome
grDevices, graphics, grid, stats, utils, ComplexHeatmap (>=
2.5.4), matrixStats, 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
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
Rcpp, basilisk, assertthat, reticulate, Rtsne, irlba
methods, graphics, grDevices, grid, utils, stats, Matrix, Rcpp
(>= 0.10.3), RcppEigen, RSpectra (>= 0.14-0), irlba,
pcaMethods, Biobase, BiocGenerics, SummarizedExperiment,
SingleCellExperiment, ggplot2, ggplot.multistats, rlang, tidyr,
tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW,
smoother, scales, scatterplot3d
Biobase, cluster, graphics, grDevices, lattice, methods, stats
Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0),
cowplot, grid, fastmatch, Matrix, scales, 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, 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
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, utils, stats, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, Biostrings, Rsamtools, BiocParallel
Rcpp, DelayedMatrixStats, matrixStats, MatrixGenerics,
DelayedArray, HDF5Array, SummarizedExperiment,
SingleCellExperiment, BiocGenerics, methods, stats, utils,
splines, rlang, vctrs
AnnotationDbi, GO.db, methods, rlang, stats, utils,
yulab.utils
methods, stats, utils, graphics, S4Vectors, IRanges, Biobase,
SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel,
BiocParallel, SingleCellExperiment, SpatialExperiment,
sparseMatrixStats, DelayedArray, DelayedMatrixStats, HDF5Array,
BiocSingular
rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>=
2.13.1), methods, GenomicRanges, abind, BiocParallel,
BatchJobs, h5vcData, GenomeInfoDb
utils, stats, tools, Matrix, rhdf5filters, BiocGenerics (>=
0.31.5), S4Vectors, IRanges, S4Arrays (>= 1.1.1)
grDevices, graphics, stats, utils, methods, statmod
data.table, grDevices, methods, RColorBrewer, Rhtslib,
survival, DNAcopy
methods, DelayedArray, Rcpp, S4Vectors, SingleCellExperiment,
SummarizedExperiment, ClusterR, benchmarkme, Matrix,
BiocParallel
methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack,
MCMCglmm, coda, magrittr, tibble, Biobase
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)
Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome,
S4Vectors, SummarizedExperiment, GenomicRanges, IRanges,
Rsamtools, GenomeInfoDb
Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
S4Vectors, tools
MsCoreUtils, PSMatch, BiocParallel, IRanges (>= 2.13.28),
plyr, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant
(>= 1.16), mzID (>= 1.5.2), digest, lattice, ggplot2, scales,
MASS, Rcpp
Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3),
ncdf4
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, zlibbioc
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
Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr,
tibble, ggplot2, tidyr
stats4, Biobase, mclust (>= 4.3), caret, e1071, sampling,
class, kernlab, lattice, nnet, randomForest, proxy, FNN,
hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales,
MASS, knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools,
plyr, ggplot2, biomaRt, utils, grDevices, graphics
methods, parallel, Matrix (>= 1.5-0), grid, annotate, graph
(>= 1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi,
IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm,
qtl, Rgraphviz
utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25),
IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops,
BiocParallel, stats
XML (>= 1.98-0), BiocGenerics (>= 0.35.3), S4Vectors (>=
0.23.18), IRanges (>= 2.13.13), XVector (>= 0.19.7),
GenomeInfoDb (>= 1.15.2), Biostrings (>= 2.47.6), zlibbioc,
curl, httr, Rsamtools (>= 1.31.2), GenomicAlignments (>=
1.15.6), BiocIO, tools, restfulr (>= 0.0.13)
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
methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors,
BiocParallel, GenomicRanges, SummarizedExperiment,
DelayedArray, DelayedMatrixStats, beachmat
methods, parallel, IRanges, GenomicRanges, GenomeInfoDb,
Biostrings, S4Vectors
Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12),
GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), pwalign,
hwriter, methods, zlibbioc, lattice, latticeExtra,
graphics, grDevices, stats, utils, BiocGenerics, zlibbioc
utils, stats, matrixStats, IRanges, XVector
Rcpp, Matrix, matrixStats (>= 0.60.0), methods
ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta, stats, graphics
MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges (>=
1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats,
data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4),
crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18
utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.27.12), IRanges
(>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.57.2),
AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome
(>= 1.47.3), GenomicFeatures (>= 1.31.3)
MSnbase (>= 2.29.3), mzR (>= 2.25.3), methods, Biobase,
BiocGenerics, ProtGenerics (>= 1.35.4), lattice,
MassSpecWavelet (>= 1.66.0), S4Vectors, IRanges,
SummarizedExperiment, MsCoreUtils (>= 1.15.5), MsFeatures,
MsExperiment (>= 1.5.4), Spectra (>= 1.13.7), progress,
jsonlite, RColorBrewer, MetaboCoreUtils (>= 1.11.2)
methods, utils, tools, zlibbioc, BiocGenerics, S4Vectors,
IRanges
cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib,
flowWorkspace
cpp11, BH(>= 1.81.0.0), cytolib, RProtoBufLib
Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR
Rhtslib (>= 2.99.1), S4Vectors, IRanges, XVector, Biostrings
S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc
S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0)
R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles
tkWidgets (>= 1.19.0), affydata, widgetTools, hgu95av2cdf
BiocStyle, rmarkdown, knitr, testthat, digest, Matrix
testthat, knitr, BiocStyle, chihaya, BiocSingular,
ResidualMatrix
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
testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
testthat, BiocStyle, knitr, rmarkdown, scran, scater,
bluster, scRNAseq
testthat, BiocStyle, knitr, rmarkdown, rcmdcheck,
BiocParallel, HDF5Array
tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr,
limma
testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy,
RcppHNSW
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
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
BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer,
EnsDb.Hsapiens.v75, RUnit
knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut,
scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans,
kohonen, apcluster, DirichletMultinomial, vegan, fastcluster
RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL,
BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs,
png,rmarkdown, BiocManager,bibtex
BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix,
BiocStyle, testthat, rmarkdown, knitr
JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat,
knitr, rmarkdown, pheatmap, motifmatchr
Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat,
BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38,
TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Ggallus.UCSC.galGal3
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
testthat, flowWorkspaceData , knitr, rmarkdown, parallel
BiocParallel, HDF5Array (>= 1.17.12), genefilter,
SummarizedExperiment, airway, lobstr, DelayedMatrixStats,
knitr, rmarkdown, BiocStyle, RUnit
knitr, rmarkdown, BiocStyle, ggplot2, uwot, testthat
knitr, rmarkdown, igraph, testthat, FNN, tidyverse,
gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq,
org.Mm.eg.db, scran, repr
lattice, parallel, MASS, RColorBrewer, xtable
knitr, tximportData, 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
affydata, tools, splines, hgu95av2cdf, hgu95av2probe
parallel, digest, Matrix, crayon, RUnit, knitr, markdown,
rmarkdown, BiocGenerics
class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer,
BiocStyle, knitr
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 (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat,
MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown,
BiocStyle, TENxPBMCData, muscData, scran, Matrix, dplyr
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
BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma,
RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny,
shinydashboard, ggplot2, data.table, plotly, future, promises,
shinybusy, shinyjs
knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt,
BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown
BiocParallel, GenomicRanges, SummarizedExperiment (>=
1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter,
GenomicFeatures, RUnit, SingleCellExperiment,
DelayedMatrixStats, genefilter
RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2),
BiocStyle
XVector, GenomicRanges, Rsamtools, GenomicAlignments,
GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset,
RUnit, BiocStyle
BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines,
affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio,
org.Hs.eg.db, vsn
berryFunctions, Biostrings, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr,
mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment,
rmarkdown, S4Vectors, pheatmap, curl
signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench
beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData,
scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown
destiny, Hmisc, knitr, Seurat, scater, testthat
Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign
testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD,
impute, norm, pcaMethods, vsn, Matrix, preprocessCore,
missForest
testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>=
1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>=
0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>=
2.5.19), rmarkdown, imputeLCMD, norm, gplots, XML, shiny,
magrittr, SummarizedExperiment
msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19),
knitr, XML, 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, forcats, testthat, BiocStyle,
SingleCellExperiment
testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, xtable,
rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr, akima,
fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals,
reshape, magick
RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db,
rlecuyer, snow, Category, GOstats
Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr
bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr,
ggplot2, mockery, BiocParallel
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
BiocParallel, SparseArray (>= 0.0.4), DelayedArray, testthat,
knitr, rmarkdown, BiocStyle
IRanges, GenomicRanges, SummarizedExperiment, Matrix,
DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle,
knitr
knitr, rmarkdown, mclust, scater, BiocStyle
BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran
Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate,
digest, crayon, knitr, markdown, rmarkdown, Rsamtools,
VariantAnnotation
BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi,
knitr
parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS,
BiocGenerics
DelayedArray, testthat, knitr, rmarkdown, BiocStyle
testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle
Hmisc, clinfun, xtable, Biobase, BiocManager
RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132,
SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats,
ggplot2, BiocStyle, knitr, magick, jsonlite, httr, rjsoncons
affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr,
testthat
BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>=
0.25.1), ncdf4, testthat (>= 3.1.9), pander, rmarkdown,
MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal,
mgcv
doMC, doMPI, doSNOW, doParallel, doRedis