a4Base, a4Preproc, a4Classif, a4Core, a4Reporting
R (>= 2.10), cluster, survival, multtest
R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics
R (>= 3.6), adductData, ExperimentHub, AnnotationHub
methods, stats, zCompositions, lattice, latticeExtra
R (>= 2.7), methods, BiocGenerics (>= 0.1.0), S4Vectors (>=
0.9.25), Biobase (>= 2.15.1), affy, makecdfenv, Biostrings,
hypergraph
R (>= 3.6), impute, doParallel, grDevices, dplyr, methods,
ComplexHeatmap
R (>= 2.5.0), methods, Biobase, BiocManager, GO.db
R (>= 2.7.0), methods, stats4, BiocGenerics (>= 0.29.2),
Biobase (>= 1.17.0), IRanges
BiocGenerics (>= 0.15.10), BiocFileCache (>= 2.99.3)
R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools,
R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel,
ellipse
R (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc
R (>= 3.4), stats, utils, methods, rmarkdown, knitr,
prettydoc, yaml
R (>= 3.5.0), Biostrings, GenomicAlignments, caTools,
GenomicRanges, grDevices, graphics, stats, utils
R (>= 4.3.0), SummarizedExperiment, S4Vectors, GenomicRanges
R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase, GO.db
R (>= 4.0.0), methods, utils, graphics, stats, generics
R (>= 4.0), reticulate, methods, SummarizedExperiment
R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz
ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel,
Biobase, metafor, methods
R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment,
GenomicRanges
R (>= 2.8.1), PolynomF, Biostrings, lattice
R (>= 3.5), GenomicRanges, cowplot, breakpointRdata
R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods
R (>= 2.14.0), Biobase, binom, methods, stats
R (>= 4.4), BiocParallel, BiocGenerics, ProtGenerics,
S4Vectors, methods, stats, stats4
R (>= 4.4), BiocParallel, matter, ontologyIndex
methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix
R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase,
utils
R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML,
ggplot2, rmarkdown
R (>= 2.10), methods, Biobase (>= 2.5.5), marray
R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods,
Biobase, CGHbase (>= 1.15.1), snowfall
R (>= 3.5.0), methods, BiocGenerics (>= 0.1.0), S4Vectors (>=
0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8),
ShortRead
R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25)
BiocParallel, ProtGenerics (>= 1.39.2), R (>= 4.5.0)
stats, utils, graphics, grDevices, datasets, base, biomaRt,
GenomicRanges, R (>= 3.1.0)
methods, BiocGenerics, S4Vectors (>= 0.47.2), IRanges,
Biostrings
R (>= 4.1.0), generics, methods, S4Vectors,
MultiAssayExperiment, BiocParallel, survival
R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d,
graphics, grDevices, stats, utils, Biobase, tools, methods
R (>= 3.6), stats, utils, graphics, infotheo, lattice,
latticeExtra, httr, jsonlite
R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats,
utils
R (>= 3.0), Biobase, methods, ff, oligoClasses, snow
R (>= 3.5.0), methods, utils, stats, graphics, parallel,
GenomicRanges
R (>= 2.10), methods, tools, stats, genefilter
brglm, doParallel, foreach, GenomicRanges, methods,
splitstackshape
R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>=
2.17.8), limma
R (>= 3.2.3), Rsamtools, GenomeInfoDb,
BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors
R (>= 4.0.0), methods, grid, graphics, stats, grDevices
R (>= 4.1), methods, AnnotationFilter, S4Vectors
R (>= 4.1), BiocGenerics, SummarizedExperiment
R (>= 4.0.0), SummarizedExperiment, S4Vectors
R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats,
LaplacesDemon, Matrix
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 (>= 1.9.3), SparseArray (>=
1.7.5)
MatrixGenerics (>= 1.15.1), DelayedArray (>= 0.31.7)
SparseArray (>= 1.5.15), DelayedArray (>= 0.31.6)
R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh,
tseries, pvclust, fBasics, grid, reshape, scales
S4Vectors (>= 0.23.18), IRanges, GenomicRanges,
SummarizedExperiment (>= 1.1.6)
R(>= 4.0.0), R.utils, DESeq2, BiocParallel
BiocParallel, Biobase, SummarizedExperiment, IRanges (>=
2.5.17), GenomicRanges (>= 1.23.7), DESeq2 (>= 1.39.6),
AnnotationDbi, RColorBrewer, S4Vectors (>= 0.23.18)
R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery,
DrugVsDiseasedata, cMap2data, qvalue
blockmodeling, gplots, testthat, R (>= 3.0.0)
R (>= 3.6.0), methods, grid, ComplexHeatmap (>= 2.11.0),
GenomicRanges
R (>= 3.6), SummarizedExperiment, MultiAssayExperiment,
cluster (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14),
flexmix (>= 2.3.15), RSKC (>= 2.4.2), sparcl (>= 1.0.4)
methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 3.99.3),
BiocFileCache (>= 2.99.3)
R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma,
S4Vectors, xml2, RCurl, jsonlite, BiocStyle
methods, LiquidAssociation, parallel, doParallel, stats,
Hmisc, utils
R (>= 3.1),FNN, psych, gtools, zoo, rgl, grid, VennDiagram
R (>= 2.15.0), methods, Biobase, rrcov, flowCore
R (>= 2.11.0), flowCore, flowViz,flowClust
R (>= 3.2), methods, flowCore, flowViz, flowStats
R (>= 2.8.0), Biobase, coda, EBarrays, mgcv
R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats,
utils
R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges
R (>= 4.1), survcomp, biomaRt, iC10, AIMS
R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter
R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate
R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods
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 (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods,
BiocGenerics (>= 0.13.8)
R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors
R (>= 4.3.0), ggplot2, ggraph, XML, igraph, tidygraph
R (>= 4.0.0), stats, methods, graphics, GGally, network, sna,
scales, matrixStats
R (>= 3.5), Matrix, MASS, locfdr, stats, utils
R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix,
base,GenomicRanges
R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0)
Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr
shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5,
R(>= 2.10.0)
R (>= 3.1.2), grid, IRanges, GenomicRanges
R (>= 4.5), methods, rhdf5, BiocGenerics, SparseArray
R(>= 4.3), QFeatures, S4Vectors, Spectra
R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods
ggfortify, R (>= 4.1), SummarizedExperiment (>= 1.16)
R (>= 4.4.0), SummarizedExperiment (>= 1.1.6), GenomicRanges,
IRanges, S4Vectors
R (>= 3.6), utils, curl, rhdf5, R6, grid
InteractionSet, GenomicRanges, SummarizedExperiment, R (>=
4.1.0)
R (>= 2.11.0), cluster, Biobase, methods
R (>= 2.9.0), Biobase, fdrtool, MASS, survival
R (>= 2.10), methods, Biobase, annotate, plotrix
R (>= 3.5.0), GenomicRanges, methods, shiny
R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1),
AnnotationHub
xcms (>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats,
utils
R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.53.2),
S4Vectors (>= 0.47.6)
R(>= 4.2.0), Matrix, parallel, BiocParallel,
SummarizedExperiment, BiocGenerics, lme4, nnls
R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser,
pd.mapping50k.xba240
R (>= 3.3.0), methods, stats, utils, graphics
R (>= 2.13.2), methods, graphics, fdrtool
R (>= 4.1), ExperimentHub, AnnotationHub
cluster, gplots, diptest, Biobase, R (>= 3.0.2)
R (>= 4.4), BiocParallel, Matrix, methods
RUnit, BiocGenerics, BiocParallel, GenomicRanges,
SummarizedExperiment
R (>= 3.3.0), stats, gplots, gtools,graphics,base,
utils,grDevices
R (>= 2.15), grDevices, graphics, methods, stats, utils
R (>= 4.0), Rsolnp, snowfall, deSolve, CNORode
R (>= 4.0), methods, CAMERA, xcms (>= 1.35)
R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea,
ggplot2, ggrepel
R (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign
R (>= 4.3.0), SummarizedExperiment, stats
R (>= 4.1), MultiAssayExperiment (>= 1.8.3)
R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment
R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase,
annotate, cluster
R (>= 4.0), SummarizedExperiment, topGO, stats
data.table, parallel, utils, stats, R (>= 4.1)
Biostrings, GenomicRanges, ggplot2 (>= 4.0.0), R (>= 4.5.0),
R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment,
limma
R (>= 2.10), methods, BiocGenerics, Biobase
R (>= 3.6), SummarizedExperiment, S4Vectors
R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods,
minet, mclust, reshape2
R (>= 3.3), Biobase, illuminaio, quadprog
R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR,
qpcR
R (>= 4.5.0), ggplot2, SummarizedExperiment
dplyr, optimalFlowData, rlang (>= 0.4.0)
R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>=
1.23.15), Biobase, vegan
R (>= 4.1.0), SummarizedExperiment, S4Vectors
R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase
R (>= 3.0.0), methods, Biobase, BiocGenerics,
R (>= 3.5), cn.mops, methods, utils, stats, graphics
graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods,
stats4
R (>= 3.6.0), Biobase, methods, annotate, Heatplus, BMA,
ggplot2, Hmisc
R (>= 4.1.0), SummarizedExperiment (>= 1.3.81)
R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods
R (>= 2.14.0), GenomicAlignments, affy, RPA
R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats,
methods, annotate
R (>= 3.2.0), oligo (>= 1.32.0),graphics,grDevices, methods,
stats, utils, mclust, oligoClasses
BiocGenerics, S4Vectors, IRanges, Biostrings (>= 2.71.5)
R (>= 3.5.0), methods, BiocGenerics, Biostrings
R (>= 4.1), MultiAssayExperiment (>= 1.33.6)
R (>= 3.5), Biostrings, pwalign, BiocGenerics, methods
R (>= 3.2.1), stats, methods, Rmpfr, gmp
BiocGenerics, DelayedArray, R (>= 4.1.0)
R (>= 3.2), Biobase, rcellminerData (>= 2.0.0)
R (>= 4.4.0), SummarizedExperiment, methods
R (>= 4.0.0), S4Vectors, dplyr, tibble, BiocSet,
SummarizedExperiment
R (>= 4.4.0), SummarizedExperiment, MultiAssayExperiment,
shinyBS, dplyr, ggplot2, htmltools, knitr, coseq
R (>= 2.6.0), methods, utils, graph, grid
R (>= 3.0.2), methods, GenomicRanges, abind
R (>= 3.6.0), Biobase, ggplot2, limma, methods
boot, SummarizedExperiment, fission, knitr, methods
methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz
R (>= 3.1.1), affy, BiocGenerics, BiocStyle, methods,
rmarkdown
R (>= 3.5.0), methods, Seqinfo, GenomicRanges (>= 1.61.1),
Biostrings (>= 2.77.2)
R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils
foreach, doParallel, parallel, Biostrings, methods, utils
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 (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
R (>= 3.5.0), Biostrings, pwalign, stringr
R (>= 3.5.0), smoothie, GenomicRanges, IRanges,
SummarizedExperiment
R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings,
GEOquery, affy, affyio, foreach, sva
R (>= 4.0), SummarizedExperiment, ComplexHeatmap
R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel,
GenomicRanges, ShortRead, stats
R (>= 3.1), AnnotationDbi, GO.db, annotate
BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>=
2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6)
R (>= 4.0.0), MLInterfaces, Biobase, e1071, BiocParallel,
survival
R(>= 4.2.0), Rcpp, SummarizedExperiment, org.Hs.eg.db
R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13),
fields, hwriter (>= 1.1), RColorBrewer, methods
R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines,
GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs
R (>= 4.0), ggplot2, ggridges, SummarizedExperiment,
BiocGenerics
R (>= 3.6.0),SummarizedExperiment, methods, Rcpp
R (>= 3.5.0), methods, Rsamtools, Biostrings, reshape,
ggplot2, RColorBrewer, stats
ggplot2 (>= 4.0.0), Rsamtools, S4Vectors
R (>= 4.0.0), methods, MatrixGenerics (>= 1.1.3),
GenomicRanges (>= 1.61.4), Biobase
SummarizedExperiment, pheatmap, survival, survminer,
clustvarsel, stats, utils
R (>= 3.2), mgcv, genefilter, BiocParallel
Rsamtools (>= 1.31.2), Biostrings, ShortRead (>= 1.37.1),
methods
methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5),
Rsamtools, hwriter
R (>= 4.3.0), SummarizedExperiment, ttservice (>= 0.5.0)
SparseArray (>= 1.5.20), DelayedArray (>= 0.31.7)
R (>= 2.12.0), data.table, impute, aroma.affymetrix
R (>= 3.6), EpiDISH, limma, nnls, quadprog
R (>= 3.4), Biobase, dplyr, magrittr, tidyr
R (>= 3.6.0), stats, utils, dplyr, methods
R (>= 2.15.0), methods, limma, anota, DESeq2, edgeR, RankProd,
topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix,
Biobase
R (>= 3.5.0), GenomicRanges, IRanges,
BSgenome.Hsapiens.UCSC.hg19
R (>= 3.5), GenomicRanges, Structstrings
R (>= 3.6), GenomicRanges, Modstrings, Structstrings, tRNA
R (>= 2.15.2), methods, BiocGenerics, Biobase
R (>= 4.2.0), methods, BiocGenerics (>= 0.51.1), S4Vectors
R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>=
1.27.6), SummarizedExperiment (>= 1.5.3)
R (>= 4.3.0), ggplot2, limma (>= 3.62.2), BiocParallel
R (>= 4.0), GenomicRanges, IRanges, ggplot2
R (>= 2.5.0), digest, tools, utils, codetools
R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma,
qvalue
R (>= 4.3.0), methods, BiocGenerics (>= 0.15.3),
SummarizedExperiment
methods, graphics, grid, Biobase, annaffy, mpm, genefilter,
limma, multtest, glmnet, gplots
methods, Biobase, ROCR, pamr, glmnet, varSelRF, utils,
graphics, stats
Biobase, graphics, grDevices, methods, multtest, stats, tcltk,
utils
ggplot2, RColorBrewer, circlize, reshape2, VennDiagram, plyr,
flexdashboard, BiocParallel (>= 1.1.25), png, grid, gridExtra,
rmarkdown, knitr, vegan, ggcorrplot, ggdendro, plotly,
BiocStyle, stringr, utils, methods, grDevices, stats, tools,
graphics
Biobase, QDNAseq, ggplot2, grid, stats, utils, methods,
grDevices, GenomicRanges
Biobase, grDevices, graphics, methods, stats, splines, utils
bit, DNAcopy, tilingArray, waveslim, cluster, aCGH
AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db
(>= 1.8.1), graphics, grDevices, KEGGREST (>= 1.30.1), multtest
(>= 1.6.0), stats (>= 2.1.0)
affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods,
preprocessCore, stats, utils
affxparser (>= 1.16.0), affy, graphics, Biobase
grDevices, graphics, stats, utils, tcltk, tkrplot, limma,
affy, affyio, affyPLM, gcrma, BiocGenerics, AnnotationDbi,
BiocManager, R2HTML, xtable
alabaster.schemas, methods, utils, S4Vectors, rhdf5 (>=
2.47.6), jsonlite, jsonvalidate, Rcpp
Rfast, BiocParallel, GenomicRanges, IRanges, S4Vectors,
SummarizedExperiment, multtest, directlabels
rmarkdown (>= 2.5), tools, methods, ggplot2 (>= 3.4.0),
GGally, dplyr, rjson, shiny, shinydashboard, DT, stats, utils,
tximport (>= 1.17.4), cowplot, rlang, Rcpp
rjsoncons (>= 1.0.1), DBI, duckdb (>= 1.3.1), rlang, curl,
BiocFileCache, spdl, memoise, BiocBaseUtils, utils, stats,
tools, methods, whisker, ggplot2
callr (>= 3.0.0.9001), Matrix, Rcpp, BiocFileCache, DT,
MultiAssayExperiment, circlize, curatedTCGAData, foreach,
glmnet, httr, limma, matrixStats, readr, reshape2, tibble,
rmarkdown, graphics, grid, parallel, stats, knitr, ggplot2,
gridExtra, utils
ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils,
plyr, DESeq2
stats, CVXR, DescTools, Hmisc, MASS, Matrix, Rdpack,
doParallel, doRNG, energy, foreach, gtools, lme4, lmerTest,
multcomp, nloptr, parallel, utils
igraph, Biobase, survival, MASS, stats, RColorBrewer
ape, assertthat, caret, covr, DESeq2, dplyr, DT, forcats,
ggforce, ggplot2, GUniFrac, lattice, limma, magrittr, Matrix,
methods, MultiAssayExperiment, plotly, rentrez, reshape2,
ROCit, S4Vectors (>= 0.23.19), scales, shiny, shinyjs, stats,
SummarizedExperiment, tibble, tidyr, tsne, umap, utils, vegan,
XML
cli, lifecycle, Matrix, methods, purrr, R6 (>= 2.4.0),
reticulate (>= 1.41.1), rlang, stats
DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice,
Rsamtools, genefilter, IRanges, BiocGenerics
Biobase, DBI, xtable, graphics, utils, stats, methods,
BiocGenerics (>= 0.13.8), httr
DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST
utils, methods, grDevices, RSQLite, BiocManager, BiocVersion,
curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr2,
yaml, dplyr, BiocBaseUtils
multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices,
graphics, stats, utils, SummarizedExperiment
stats, utils, methods, futile.logger, GCPtools, jsonlite,
httr, rapiclient, yaml, tibble, shiny, DT, miniUI, htmltools,
BiocBaseUtils
AnVILBase, BiocBaseUtils, curl, httr2, jsonlite, methods,
rjsoncons, tibble, utils
httr, httr2, dplyr, jsonlite, methods, tibble
methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr,
dplyr, lubridate, plotly, ggplot2
AnVILBase, BiocBaseUtils, dplyr, GCPtools (>= 0.99.4), httr,
jsonlite, methods, rlang, stats, tibble, tidyr, utils
AnVIL, AnVILGCP, BiocBaseUtils, BiocManager, httr, jsonlite,
rmarkdown, yaml, readr, whisker, tools, utils, stats
AnVIL, dplyr, jsonlite, rlang, tibble, tidyr, utils, methods,
plyr, stringr
emdbook, SummarizedExperiment, GenomicRanges, methods, stats,
utils, Rcpp
oligo, limma, httr, utils, jsonlite, rlang, tools, methods
graphics, grDevices, grid, gridBase, hexbin, limma, marray,
methods, RColorBrewer, stats, utils
AnnotationDbi, bit64, circlize, cluster, corrplot, data.table,
dplyr, getopt, ggdendro, ggplot2, gplots, ggrepel, graphics,
grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db,
pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats,
stringr, tidyr, UpSetR, utils, VennDiagram, yaml
Biostrings, GenomicRanges, IRanges, graphics, grDevices,
methods, stats, utils
gplots, graphics, grDevices, msm, Rlab, stats, sva, utils,
ggplot2, yaml
Biobase, limma, cluster, GOstats, graphics, stats,
reactome.db, KEGGREST, org.Hs.eg.db, utils, methods
DelayedArray, DelayedMatrixStats, data.table, graphics,
grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats,
SummarizedExperiment, BiocGenerics, utils
abind, arrow, BiocFileCache, BiocGenerics, bit64, cluster,
codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce,
ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma,
lme4, magrittr, matrixStats, methods, MultiAssayExperiment,
parallel, RColorBrewer, rlang, R.utils, readxl, S4Vectors,
scales, stats, stringi, SummarizedExperiment, survival, tidyr,
tidyselect, tools, utils, vsn
dplyr, Peptides, progress, purrr, ranger, rlang, stats,
stringr, tidyr, toOrdinal, utils
GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy,
reshape2, scales, coda, foreach, ggplot2, methods, utils,
graphics, stats
methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges,
GenomicRanges
Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel,
foreach, methods, stats, graphics, ggplot2, DRIMSeq,
BiocParallel
Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr,
knitr, methods, BiocParallel, robustbase, BiocStyle,
ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils,
grDevices, rlang, RColorBrewer, gtools, gridExtra, coda (>=
0.19-4)
magrittr, tidyr, dplyr, grid, circlize, ComplexHeatmap,
ggplot2, logistf, limma, stats, igraph, utils, data.table,
S4Vectors, SummarizedExperiment
ggplot2, stringr, XML, raster, dplyr, data.table, tidyr,
magrittr, DT, lazyeval, ShortRead
edgeR, GenomicRanges, abind, parallel, graphics, stats, utils
methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics,
Matrix, Rcpp
methods, beachmat, HDF5Array, DelayedArray, Rcpp
methods, beachmat, tiledb, TileDBArray, DelayedArray, Rcpp
futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp,
abind, stats, graphics, utils, methods, dixonTest, ids
cli, edgeR, BiocParallel, methods, progressr, stats,
SummarizedExperiment, utils
cluster, comprehenr, foreach (>= 1.5.2), invgamma, iterators
(>= 1.0.14), janitor (>= 2.2.0), limma (>= 3.46.0), logging (>=
0.10-108), sva (>= 3.38.0), SummarizedExperiment, methods,
BiocParallel
stats, ggplot2, scales, methods, pROC, foreach, doParallel,
parallel, cowplot, dplyr, tidyr, tidyselect, stringr, utils
dplyr (>= 1.0), tidyr, ggplot2 (>= 3.4.1), shiny (>= 1.6),
tibble, ComplexHeatmap, bslib, rlang, circlize, stats, grid,
methods, cowplot, Hmisc, sortable, shinyjqui, grDevices,
scales, DT, SummarizedExperiment, S4Vectors
BiocBaseUtils, BiocGenerics, BiocIO, curl, GenomicRanges,
IRanges, methods, Rsamtools, S4Vectors, Seqinfo, stats, utils,
XVector
BiocGenerics, pak, cli, glue, gert, gh, gitcreds, httr,
usethis, dplyr, purrr, tibble, methods, rprojroot, stringr,
yaml, tools, utils, rlang, quarto, renv
DT, shiny, jsonlite, graph, tidyr, visNetwork, dplyr, utils,
methods, BiocBaseUtils
methods, stats, utils, dplyr, RSQLite, DBI, filelock, curl,
httr2
Rgraphviz, geneplotter, graph, BiocGenerics, methods
reticulate, basilisk, BiocFileCache, methods, dplyr,
BiocGenerics
AnnotationHub, ExperimentHub, DT, htmlwidgets, rclipboard,
S4Vectors, shinyAce, shinybiocloader, shinyjs, shinythemes,
utils
stats, utils, futile.logger, parallel, snow, codetools
methods, tibble, utils, rlang, plyr, S4Vectors, BiocIO,
AnnotationDbi, KEGGREST, ontologyIndex, tidyr
BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray,
BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat (>=
2.25.1)
bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils,
yaml, BiocManager
BiocManager, fs, glue, rlang, styler, usethis (>= 2.0.1)
Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools,
utils, XML, RCurl, RUnit, BiocManager
BiocStyle, bookdown, git2r, httr, knitr, rmarkdown,
rstudioapi, stringr, tools, utils, usethis
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
AnnotationDbi, BiocFileCache, curl, httr2, progress, stringr,
utils, xml2
WGCNA, dynamicTreeCut, ggdendro, matrixStats, sva,
RColorBrewer, ComplexHeatmap, ggplot2, rlang, ggrepel,
patchwork, reshape2, igraph, ggnetwork, intergraph, NetRep,
stats, grDevices, utils, methods, BiocParallel, minet, GENIE3,
SummarizedExperiment
igraph (>= 1.0.1), AnnotationDbi, Biobase
methods, utils, grDevices, stats, crayon
stats, methods, dplyr, tibble, ggplot2, ggsci, superheat,
assertthat, drtmle (>= 1.0.4), S4Vectors, BiocGenerics,
BiocParallel, SummarizedExperiment, limma
grid, stats, grDevices, utils, circlize, viridis,
RColorBrewer, ComplexHeatmap, SummarizedExperiment, pasilla
SummarizedExperiment, ExperimentHub, methods, grid, graphics,
stats, grDevices, circlize, testthat, ComplexHeatmap(>=
1.99.8), ggplot2, matrixStats, gtools, reshape2,
preprocessCore, randomcoloR, V8, limma
stats, methods, utils, cluster, Matrix, Rcpp, igraph,
S4Vectors, BiocParallel, BiocNeighbors
Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, Seqinfo,
S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage,
utils, HiCBricks
CellNOptR, matrixStats, snowfall, Rgraphviz, cluster,
flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods,
utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown
methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>=
1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2,
BiocGenerics, gtools, doParallel, foreach
methods, Biobase, tidyselect, dplyr, ggplot2, magrittr, rlang,
stringr, withr, edgeR, ComplexHeatmap, impute (>= 1.80.0),
data.table (>= 1.16.0), RColorBrewer (>= 1.1-3), circlize (>=
0.4.16), ggrepel (>= 0.9.6), e1071 (>= 1.7-8),
SummarizedExperiment, utils
dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel,
crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs
GenomicRanges, methods, rlang, S4Vectors, utils
devtools, stringi, gtools, stats, utils, SummarizedExperiment,
Biostrings, IRanges
utils, methods, Matrix, S4Vectors, IRanges
gplots, methods, grDevices, stats, SummarizedExperiment
doParallel, ggplot2, gplots, graphics, grid, gtable, knnmi,
MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats,
SummarizedExperiment
checkmate, dplyr, ggplot2, magrittr, openxlsx, scales,
SummarizedExperiment, tidyr
methods, xcms, RBGL, graph, graphics, grDevices, stats, utils,
Hmisc, igraph
ggplot2, dplyr, org.Hs.eg.db, vcfR, clusterProfiler, stringr,
DT, MesKit, maftools, data.table, utils, stats, methods, tidyr
CardinalIO, Biobase, EBImage, graphics, grDevices, irlba,
Matrix, matter (>= 2.7.10), nlme, parallel, utils
readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson,
rmarkdown
utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI
AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1),
GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29),
methods, grDevices, utils
ggplot2, magrittr, graphite, ggraph, igraph, bnlearn (>= 4.7),
patchwork, org.Hs.eg.db, clusterProfiler, utils, enrichplot,
reshape2, ggforce, dplyr, tidyr, stringr, depmap,
ExperimentHub, Rmpfr, graphlayouts, BiocFileCache, ggdist,
purrr, pvclust, stats, rlang
utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite,
rapportools, basilisk, reticulate, shinyBS, shinycssloaders,
rintrojs, rlang, markdown
plyr, tidyr, dplyr, ggplot2, forcats, ggraph, igraph,
scatterpie, circlize, ComplexHeatmap, tibble, grid, ggbump,
stringr, ggtext, ggh4x, patchwork, RColorBrewer, scales,
viridis, grDevices, graphics, stats, methods
methods, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr,
ggplot2, stringr, magrittr, ShortRead (>= 1.48.0), Biostrings
(>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors, seqinr,
Rsamtools
methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils,
Rsamtools, BiocParallel, foreach, utils, parallel, doParallel
AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid,
mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats,
topGO, utils
base, ggplot2, ggforce, ggtree, patchwork, ape, methods, Rcpp
(>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>=
2.18.1), rstantools (>= 2.4.0), stats, utils, scales
tiff, graphics, stats, utils, reshape2, parallel, doParallel,
grDevices, matrixStats, FME, SpatialTools, sp, vioplot,
FactoMineR, Hmisc
httr, curl, utils, tools, cli, shiny, DT, rjsoncons
methods, scales, dplyr, data.table (>= 1.9.4), WGCNA, grid,
ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler,
fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools,
pracma, intergraph, grDevices, utils, network, matrixStats,
ggdendro, gridExtra, gtable, fastcluster
BiocParallel, broom.mixed, dirmult, dplyr, edgeR,
fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp,
purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment,
survival, tibble, tidyr, utils
furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr,
future, stats
circlize, ComplexHeatmap, clusterProfiler, DESeq2, dplyr,
GenomicTools.fileHandler, GGally, ggnetwork, ggplot2, ggpubr,
ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3,
stats, SummarizedExperiment, S4Vectors, utils, methods
Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges,
magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats,
rlang
Rcpp, utils, GenomicRanges, basilisk, R.utils, stats,
cfToolsData, grDevices, graphics
Biobase, CGHbase, CGHcall, methods, stats, utils
rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp
(>= 0.11.0), ggplot2,grid,gridExtra,
png,base64enc,DT,rsvg,jsonlite,stringi
matrixStats, MASS, Hmisc, Delaporte, methods, grDevices,
graphics, stats, utils
methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges,
ShortRead
Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14),
graphics, grDevices, HilbertVis, ShortRead, stats, timsac,
utils
IRanges, XVector, Biostrings, ShortRead, graphics, methods,
stats, utils
Biobase, GEOquery, frma, affy, bigmemory, biganalytics
graphics, stats, utils, methods, survival
methods, S4Vectors, MsCoreUtils (>= 1.7.5), Spectra
XML, RCurl, RBGL, parallel, foreach, doParallel, openxlsx,
igraph, circlize, graph, stats, utils, grDevices, graphics,
methods, biomaRt, rJava
dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork,
ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat,
tidygraph, expm, Matrix
grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2
(>= 3.5.0), ggpubr, reshape2, ggupset, broom, dcanr
shiny, ggraph, igraph, ggiraph, cowplot, htmlwidgets, readxl,
dplyr, readr, purrr, tibble, patchwork, R.utils, shinyWidgets,
colorspace, shinyhelper, shinycssloaders, ggnewscale,
shinydashboard, DT, colourpicker, grDevices, methods, utils,
stats, ggplot2, magrittr, tools
Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, coop,
slam, matrixStats, methods
mzR, S4Vectors, dbscan, RColorBrewer, ape, network, GGally,
ggplot2, plotly, methods, utils, stats, sna, grDevices,
graphics, Biobase, gplots, MSnbase
FactoMineR, bigstatsr, clValid, doSNOW, parallel, foreach,
dplyr, fpc, mice, modeest, flock, networkD3, methods,
ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices,
ggplot2, grid, stats, utils, pbapply
AnnotationDbi, DOSE (>= 3.23.2), dplyr, enrichplot (>= 1.9.3),
GO.db, GOSemSim (>= 2.27.2), gson (>= 0.0.7), httr, igraph,
magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils,
yulab.utils (>= 0.1.6)
methods, pracma, princurve (>= 2.0.5), scatterplot3d,
RColorBrewer, grDevices, graphics, utils, stats
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
methods, rhdf5, data.table, flowCore, SummarizedExperiment,
matrixStats
DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice
BiocGenerics, Biobase, IRanges, Rsamtools, Seqinfo, S4Vectors
BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq,
IRanges, Rsamtools, foreach, ggplot2, plyr, GenomeInfoDb,
gplots, reshape2, stringr, testthat, graphics, methods, shiny,
shinyFiles, shinyjs, grid, openxlsx
methods, class, gplots, mclust, amap, apcluster, foreach,
parallel, doParallel, fastcluster, corrplot, biwt, Biobase,
reshape2, stringr, tibble, tidyr, dplyr, devtools
utils, graphics, stats, methods, reshape2, ggplot2, scales,
ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite,
Biostrings
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
ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix (>=
1.6.0), BB, reshape2, alabama, cobs, Biobase, vegan, grDevices,
graphics, methods, SummarizedExperiment
methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr,
knitr, abind, clue, grDevices, utils, pdist, magrittr,
reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach,
coda
knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots,
gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr,
modeest, edgeR, limma, vioplot, methods, stats, utils, ape,
phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny,
shinydashboard
circlize (>= 0.4.14), GetoptLong, colorspace, clue,
RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges,
matrixStats, foreach, doParallel, codetools
BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr,
RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges,
Spectra (>= 1.15.10), MsCoreUtils, MetaboCoreUtils,
BiocParallel, stringi
data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr,
rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio,
scales, shinydashboard, shinyjs, stats, tibble, grid
stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra,
utils, data.table
matrixStats, gplots, grDevices, methods, graphics, stats,
utils
Biobase, ALL, graphics, stats, utils, cluster
fastICA (>= 1.2.1), sm, org.Hs.eg.db, GO.db, stats,
SummarizedExperiment, BiocParallel, graph, ggplot2, methods,
Rfast, pheatmap, survival, topGO, graphics, grDevices
methods, stats, utils, Biostrings, Biobase, dplyr, stringr,
purrr, ggplot2, data.table
Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics,
piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods,
stats, utils, graphics, grDevices, lsa, data.table, crayon,
glue, rlang, bench
edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2,
scales, HTSFilter, corrplot, HTSCluster, grDevices, graphics,
stats, methods, compositions, mvtnorm
CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr,
rlang, stringr, utils, visNetwork, decoupleR
rmarkdown (>= 2.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr,
ggplot2, grDevices, tools, SummarizedExperiment, genefilter,
DT, GenomeInfoDbData, caTools, randtests, stats, utils,
methods, ragg
parallel, genefilter, grDevices, stats, graphics
SummarizedExperiment, grDevices, reshape2 , survival ,
survminer , ggplot2 , MTLR , glmnet , rms , preprocessCore ,
Matrix , stats, Hmisc, ggfortify, randomForestSRC, caret,
SurvMetrics, MASS,
splines, graphics, nor1mix, stats, quantreg
BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges,
S4Vectors, stringr
basilisk (>= 1.9.2), BiocGenerics, Biostrings, IRanges,
methods, randomForest, reticulate, stringr, utils, XVector
AnnotationDbi, BiocParallel, Biostrings, methods,
GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices,
grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>=
0.9.38), utils
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
WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp
RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils,
grid, gridExtra, methods, stats, BiocFileCache
AnnotationDbi, AnnotationHub, binr, cowplot, data.table,
dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics,
highcharter, htmltools, httr, limma, methods, parallel,
pbapply, purrr, qs, R.utils, readxl, reshape2, rhdf5, rlang,
scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble,
tools, utils
ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils
AnnotationHub, RSQLite, XML, utils, ChemmineR, methods, stats,
rappdirs, BiocFileCache
Biobase, flowCore, flowDensity, flowClust, cytometree,
ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats,
utils
stats, abind, sirt, MASS,TOAST, tibble, parallel,
preprocessCore, SummarizedExperiment, TCA, PROPER,
methods,dplyr, utils, RColorBrewer, graphics, edgeR,
BiocParallel, checkmate, mvtnorm, DESeq2, rlang, e1071
doParallel, dplyr, glmnet, rpart, rpart.plot, stats,
flowCore,grDevices, graphics, utils
CytoGLMM, diffcyt, DT, dplyr, ggplot2, magrittr, methods,
rlang, stats, shiny, shinyFeedback, shinyjs, shinyMatrix,
SummarizedExperiment, tibble, tidyr
stats, methods, BiocParallel, RColorBrewer, cowplot,
doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr,
mbest, pheatmap, stringr, strucchange, tibble, ggrepel, MASS,
logging, Matrix, tidyr, caret, rlang, grDevices
Rcpp, SummarizedExperiment, utils, methods, ComplexHeatmap,
circlize, ashr, data.table, BiocParallel, dplyr, stats,
magrittr, rlang, S4Vectors
methods, stats, rlang, pracma, withr, flowCore, reshape2,
ggplot2, ggrepel, ggforce, patchwork, transport, smacof,
BiocParallel, CytoPipeline
gplots, tools, flowCore, grDevices, stats, utils, matrixStats,
methods
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, stats, utils, withr, rlang, ggplot2 (>= 3.4.1),
ggcyto, BiocFileCache, BiocParallel, flowCore, PeacoQC, flowAI,
diagram, jsonlite, scales
Biobase, MSnbase, DAPARdata (>= 1.30.0), utils, highcharter,
foreach
igraph, foreach, plyr, stringr, reshape2, methods, Matrix,
graphics, stats, RColorBrewer, circlize, doRNG
MCMCpack, matrixStats, robustbase, aod, e1071
Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice,
BiocGenerics
plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore,
flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks
CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr,
matrixStats, methods, patchwork, parallel, pbapply, reshape2,
rlang, scattermore, stats, statmod, survey, tibble, viridisLite
methods, DBI, S4Vectors, IRanges, XVector
BiocParallel, broom, dplyr, magrittr, Matrix, parallelly,
purrr, rlang, stats, stringr, tibble, tidyr, tidyselect, withr
tensorflow, CatEncoders, matlab, rcdk, stringdist, tokenizers,
webchem, purrr, ttgsea, PRROC, reticulate, stats
fgsea, ggplot2, stringr, ggpubr, BiocParallel, pROC, stats,
grDevices, graphics, depmap, readr, dplyr
checkmate, data.table, DESeq2, edgeR (>= 3.13.4),
GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment
graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL,
Rgraphviz, rrcov, NCIgraph
utils, methods, Biobase, BiocGenerics, broom, circlize,
ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster,
dendextend, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid,
ggrepel, grDevices, knitr, logging, magrittr, psych,
RColorBrewer, reshape, rlang, scales, stats, stringr, stringi,
S4Vectors, SummarizedExperiment, tidyr, tibble
graphics, grDevices, methods, stats, utils
methods, sparseMatrixStats (>= 1.13.2), Matrix (>= 1.5-0),
S4Vectors (>= 0.17.5), IRanges (>= 2.25.10), SparseArray (>=
1.5.19)
methods, utils, S4Arrays, SparseArray, DelayedArray (>=
0.31.8), HDF5Array, BiocSingular, rTensor, DelayedRandomArray
(>= 1.13.1), irlba, Matrix, einsum,
IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2,
tictoc
stats, MASS, Matrix, ggplot2, gridExtra, methods
Rcpp, basilisk, assertthat, reticulate, Rtsne, irlba
IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2)
BiocGenerics (>= 0.7.5), Biobase, BiocParallel, matrixStats,
methods, stats4, locfit, ggplot2 (>= 3.4.0), Rcpp (>= 0.11.0),
MatrixGenerics
graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq,
stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix,
jsonlite, tools, DESeq2, methods
BiocGenerics, data.table(>= 1.11.8), Seqinfo, GenomicRanges,
methods, S4Vectors, SummarizedExperiment, stats, utils
Biobase, GEOquery, impute, limma, pheatmap, plyr, scales,
snpStats, sva, swamp, stats, methods, utils, bnstruct,
RColorBrewer, grDevices
BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools,
statmod, geneplotter, genefilter
BiocGenerics, methods, rlang, S4Vectors, tidyselect
stats, DiffCorr, psych, igraph, BiocGenerics
flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma,
edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats,
methods, utils, grDevices, graphics, ComplexHeatmap, circlize,
grid
graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils
grDevices, stats, methods, Matrix, MASS, checkmate, expm,
igraph, Rcpp, RcppArmadillo, RcppParallel, plyr, precrec
BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, edgeR,
GenomicRanges, ggplot2, Matrix, methods, rlang, stats, stringr,
tibble, tidyr, tidyselect
Rcpp, Biobase, stats, biwt, gtools, MASS, tools, dplyr,
methods, utils
matrixTests, matrixStats, MetaCycle (>= 1.2.0), data.table,
ggplot2, ggExtra, dplyr, broom, shiny, shinyBS,
shinycssloaders, shinydashboard, shinyjs, BiocStyle, rmarkdown,
knitr, kableExtra, magick, VennDiagram, UpSetR, heatmaply,
viridis, plotly, DT, gridExtra, methods, stats,
SummarizedExperiment, BiocGenerics, S4Vectors, zip, reshape2
Matrix, MASS, RcppRoll,GenomicRanges, IRanges, Seqinfo,
methods, mvtnorm, stats, parallel
dplyr, tidyr, numbers, purrr, stringr, stats, utils, methods,
Rcpp (>= 0.11.2), BH
BiocParallel, dplyr, gdata, glasso, igraph (>= 2.0.3),
janitor, Matrix, methods, netgsa, stats, stringr, utils,
SummarizedExperiment
biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid,
igraph, Matrix, methods, plyr, stats, utils, magrittr, purrr,
dplyr
sva, impute, digest, mnormt, methods, grDevices, graphics,
stats, SummarizedExperiment, utils
methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy,
limma, stringr, ggplot2, graphics, grDevices, calibrate,
corrgram, gridExtra, DT, shiny, shinydashboard, readxl,
prodlim, matrixStats
AnnotationDbi, BiocParallel, fgsea, ggplot2, GOSemSim (>=
2.31.2), methods, qvalue, reshape2, stats, utils, yulab.utils
(>= 0.1.6)
edgeR, methods, stats, graphics, matrixStats, mclust, lme4,
RUnit, SummarizedExperiment, digest, S4Vectors
utils, stats, MASS, GenomicRanges, IRanges, S4Vectors,
BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2,
reshape2
annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit,
BiocGenerics, xtable
zoo, ggplot2, purrr, reshape2, parallel, IRanges, S4Vectors,
rlang, grDevices, stats, utils
BiocParallel, SummarizedExperiment, utils, ggplot2, dplyr,
tidyr, RColorBrewer, magrittr, gganimate, purrr, aricode
progeny, easierData, dorothea (>= 1.6.0), decoupleR,
quantiseqr, ROCR, grDevices, stats, graphics, ggplot2, ggpubr,
DESeq2, utils, dplyr, tidyr, tibble, matrixStats, rlang,
BiocParallel, reshape2, rstatix, ggrepel, magrittr, coin
clusterProfiler, dplyr, forcats, ggplot2, magrittr, rlang,
stats, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, vctrs (>=
0.6.4), BiocStyle
Biobase (>= 2.64.0), BiocFileCache (>= 2.12.0), BiocGenerics
(>= 0.50.0), BiocParallel (>= 1.38.0), biomaRt (>= 2.60.1),
Biostrings (>= 2.77.2), edgeR (>= 4.2.1), Seqinfo,
genomeIntervals (>= 1.60.0), GenomicAlignments (>= 1.45.1),
GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1),
graphics, IRanges (>= 2.38.1), LSD (>= 4.1-0), methods,
parallel, rappdirs (>= 0.3.3), Rsamtools (>= 2.25.1), S4Vectors
(>= 0.42.1), ShortRead (>= 1.62.0), utils
Biobase, cluster, graphics, grDevices, lattice, methods, stats
BiocGenerics (>= 0.7.1), graphics, grDevices, stats, abind,
tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils,
htmltools, htmlwidgets, RCurl
methods, splines, sva, qvalue(>= 1.99.0), MASS
gplots, Biobase, GEOquery, limma, impute, RColorBrewer, zoo,
igraph, plyr, MASS, RCurl, methods
snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl,
digest, BiocGenerics, RcppAnnoy (>= 0.0.9)
graphics, stats, GenomicRanges, S4Vectors, IRanges, limma,
edgeR (>= 4.0), methods, SummarizedExperiment, BiocGenerics,
utils
emdist, BiocParallel, matrixStats, ggplot2, CDFt,
preprocessCore
survivalROC, glmnet, rms, mboost, Matrix, igraph, methods,
survivalsvm, ggplot2, boot, e1071, survival, BiocFileCache
BiocGenerics, Rgraphviz, hash, S4Vectors, dplyr, ggplot2,
graph, magrittr, methods, pheatmap, graphics, utils, purrr,
tidyr, stats
matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize
(>= 0.4.5), IRanges
aplot (>= 0.2.1), DOSE (>= 3.31.2), ggfun (>= 0.1.7),
ggnewscale, ggplot2 (>= 3.5.0), ggrepel (>= 0.9.0), ggtangle
(>= 0.0.5), graphics, grid, igraph, methods, plyr, purrr,
RColorBrewer, reshape2, rlang, stats, utils, scatterpie,
GOSemSim (>= 2.31.2), magrittr, ggtree, yulab.utils (>= 0.1.6)
gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, DOSE,
igraph, reshape2, methods
stats, methods, utils, data.table, BiocGenerics,
GenomicRanges, Rcpp
MASS, e1071, quadprog, parallel, stats, matrixStats, stringr,
locfdr, Matrix
BoutrosLab.plotting.general, BoolNet, e1071, gtools, stats,
igraph, utils, lattice, latticeExtra, RColorBrewer, pcalg,
minet, grDevices, graph, mnem, latex2exp
EpipwR.data, ExperimentHub (>= 2.10.0), ggplot2
GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors,
IRanges, graphics, plotrix, grDevices, stats, methods
BiocParallel, data.table, matrixStats, stats, survival,
igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid,
bigmemory, graphics, utils
edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr,
qvalue, reshape2, ROCR, scales, stringr, knitr
mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils,
grDevices, methods
corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2,
ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class,
prabclus, mclust, kableExtra, dplyr, dendextend (>= 1.16.0)
shiny (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr,
magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales,
tibble, MASS, limma, S4Vectors, shinyjs, rlang
methods, graphics, grDevices, stats, utils
BiocParallel, brio, cli, curl (>= 6.0.0), data.table, httr2
(>= 1.0.0), MCMCpack, methods, openEBGM, rlang, rvest, tools,
utils, vroom, xml2
gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey
methods, shiny, stats, IRanges, Biostrings, ShortRead, DT,
S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12)
ape, data.table, dynamicTreeCut, methods, R.utils, rJava,
stats, stringr, utils
methods, graphics, grDevices, stats, BiocGenerics, S4Vectors,
IRanges
tcltk, graphics, grDevices, stats, utils
pheatmap, MASS, pracma, stats, SummarizedExperiment, methods
openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes,
forcats, RColorBrewer, RCy3, utils, stats
methods, igraph, Matrix, KEGGREST, plyr, stats, graphics,
utils
tools, methods, assertthat, rlang, dplyr, tidyr, tidyselect,
tibble, purrr, readr, stringr, httr2, rvest, progress,
BiocFileCache, shiny, ggplot2
graph, stats, e1071, methods, gRbase, jsonlite, BiocFileCache,
curl, igraph
igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2,
RColorBrewer, png, methods, stats, utils, graphics, grDevices
Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0),
cowplot, grid, fastmatch, Matrix, scales, utils
foreach, doParallel, GenomicRanges, IRanges, Rsamtools,
parallel, S4Vectors
Biobase, BiocParallel, parallel, stats, SummarizedExperiment,
survival, utils
data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils
gplots, graphics, MASS, methods, SparseM, stats, utils
ggplot2, flowCore, plyr, changepoint, knitr, reshape2,
RColorBrewer, scales, methods, graphics, stats, utils,
rmarkdown
colorRamps, abind, BiocParallel, graphics, stats, utils,
plotly, shiny
methods, flowCore, EBImage, vegan, hexbin, ggplot2, grid
BiocGenerics, methods, Biobase, graph, flowCore, parallel
Biobase, BiocGenerics (>= 0.29.2), grDevices, graphics,
methods, stats, utils, stats4, Rcpp, matrixStats, cytolib (>=
2.13.1), S4Vectors
flowDensity (>= 1.13.1), Cairo, e1071, grDevices, graphics,
stats,methods
flowCore, graphics, flowViz (>= 1.42), car, polyclip, gplots,
methods, stats, grDevices
Biobase, BiocGenerics (>= 0.1.6), graphics, grDevices,
methods, stats, stats4
effsize, furrr, future, purrr, ggiraph, ggrepel, ggplot2,
igraph, Matrix, matrixStats, stats, utils, visNetwork,
htmlwidgets, grDevices, methods, stringr, stringi, Rdpack,
data.table (>= 1.9.5), gridExtra,
Biobase, graphics, grDevices, methods, rrcov, stats, feature,
flowCore
rrcov,flowCore, graphics, methods, stats, utils
flowCore, car, caTools, knitr, rmarkdown, minpack.lm, shiny,
methods, graphics, stats, utils
stats, utils, colorRamps, ConsensusClusterPlus, dplyr,
flowCore, ggforce, ggnewscale, ggplot2, ggpubr, grDevices,
magrittr, methods, rlang, Rtsne, tidyr, BiocGenerics, XML
BiocGenerics, MASS, flowCore (>= 1.99.6), flowWorkspace,
ncdfFlow(>= 2.19.5), flowViz, fda (>= 2.2.6), Biobase, methods,
grDevices, graphics, stats, cluster, utils, KernSmooth,
lattice, ks, RColorBrewer, rrcov, corpcor, mnormt, clue
utils, dplyr (>= 1.0.0), tibble, magrittr, plyr, rlang
flowCore, methods, flowViz, stats, flowClust
stats4, Biobase, flowCore, graphics, grDevices, grid,
KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer,
stats, utils, hexbin,IDPmisc
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
clisymbols, crayon, dplyr, fgsea, ggplot2, ggraph, magrittr,
ontologyIndex, purrr, RecordLinkage, stringr, textclean,
tictoc, tidygraph, tidyr, vroom
Biobase, MASS, DBI, affy, methods, oligo, oligoClasses,
preprocessCore, utils, BiocGenerics
Biobase, DBI, methods, preprocessCore, stats, utils
NMF, pathifier, stats, KEGGREST, AnnotationDbi, org.Hs.eg.db,
dplyr, stringr
psych, FCPS, analogue, coop, pheatmap, ggplotify, fastcluster,
fpc, ggplot2, stringr, ggpubr, proxy, cluster, diptest,
methods, SummarizedExperiment, stats, S4Vectors
splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP
data.table, igraph, BioNet, plyr, methods, XML, sna,
intergraph, network, GGally, grid, ggplot2, mwcsr, pryr,
htmlwidgets, htmltools, shinyCyJS (>= 1.0.0)
AnVILBase, BiocBaseUtils, dplyr, httr, rlang, tibble, tidyr,
utils
Biobase, limma, RobustRankAggreg, ggplot2,
SummarizedExperiment, grid, rmarkdown, grDevices, graphics,
methods, ComplexHeatmap, stats, utils, parallel
Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector,
Biostrings (>= 2.11.32), splines, BiocManager
BumpyMatrix, BiocParallel, checkmate, futile.logger, gDRutils
(>= 1.7.1), MultiAssayExperiment, purrr, stringr, S4Vectors,
SummarizedExperiment, data.table
assertthat, BumpyMatrix, checkmate, CoreGx, PharmacoGx,
data.table, futile.logger, gDRutils (>= 1.7.1), magrittr,
methods, MultiAssayExperiment, readxl, rio, S4Vectors, stats,
stringi, SummarizedExperiment, tibble, tools, utils, XML, yaml,
openxlsx
BiocParallel, BumpyMatrix, checkmate, data.table, digest, drc,
jsonlite, jsonvalidate, methods, MultiAssayExperiment,
S4Vectors, stats, stringr, SummarizedExperiment, qs, utils
tcltk, ggplot2, methods, stats, grDevices, graphics, utils
dplyr, grDevices, ggplot2, magrittr, mixtools, scales,
pbmcapply, parallel, stats, utils
magrittr, glue, memoise, jsonlite, data.table, rlang,
lubridate, utils, stringr, SummarizedExperiment, Biobase,
tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat,
digest, R.utils, kableExtra, base64enc
graphics, grDevices, methods, stats, tcltk, utils, xtable
utils, methods, stats, Biobase, BiocGenerics
MatrixGenerics (>= 1.11.1), AnnotationDbi, annotate, Biobase,
graphics, methods, stats, survival, grDevices
amap, impute, mclust, limma, graphics, stats, utils,
iC10TrainingData
plyr, graph, htmlwidgets, Rgraphviz, RCy3, rjson, XML,
methods, grDevices, stats, graphics
igraph, snow, ape, grDevices, graphics, stats, utils,
data.table
AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats,
utils
S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser,
RColorBrewer, Biostrings
Biostrings, BiocGenerics, BiocParallel, Seqinfo,
GenomicRanges, IRanges, matrixStats, XVector, dplyr,
data.table, parallel, doParallel, foreach, methods, S4Vectors,
stats, numbers, utils
Seqinfo, GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14),
S4Vectors (>= 0.7.10)
methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, Biostrings, Rsamtools, BiocParallel, cigarillo
(>= 0.99.2)
data.table, ggplot2, reshape2, methods, utils, Biostrings,
plyr, dplyr, scales, broom, GenomeInfoDb, stats
stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache,
IRanges (>= 2.3.23), Biostrings, Seqinfo, GenomeInfoDb (>=
1.45.5), AnnotationHub, rhdf5, DelayedArray, HDF5Array
ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr,
dplyr, plotly, BiocFileCache, grid, flextable, irlba
methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges
(>= 2.19.13), data.table, stats4, stats, utils
tensorflow, word2vec, DeepPINCS, ttgsea, CatEncoders,
reticulate, stats
Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods,
graphics, stats, testthat, GeomxTools, NanoStringNCTools
xml2, rvest, stringr, RCurl, doParallel, foreach, plyr
BiocGenerics, rjson, readxl, EnvStats, reshape2, methods,
utils, stats, data.table, lmerTest, dplyr, stringr, grDevices,
graphics, GGally, rlang, ggplot2, SeuratObject
readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr,
limma, curl, rentrez, R.utils, stringr, SummarizedExperiment,
S4Vectors, rvest, httr2
utils, data.table, plyr, cqn, topconfects, stats,
SummarizedExperiment, methods
repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods,
Biobase, XML, rhdf5, digest, iterators
grDevices, graphics, methods, stats, utils, dbscan,
fastcluster, matrixStats
bslib (>= 0.6.0), BiocStyle, ComplexHeatmap, dplyr, DT,
ggbeeswarm, ggplot2, htmltools, magrittr, shiny,
SummarizedExperiment, tibble, tidyselect, tidyr
DESeq2, dplyr, edgeR, ggrepel, glue, janitor, limma, magrittr,
methods, purrr, rlang, scales, stats, stringr, tibble, tidyr
plyr, scales, hexbin, data.table, RColorBrewer, gridExtra,
rlang
BiocFileCache, data.table, dplyr, magick, patchwork,
shadowtext, stringr, tibble, methods, utils, stats, grDevices,
gtable
Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot,
RColorBrewer, ggfun (>= 0.2.0), ggforce, dplyr, R4RNA,
grDevices, seqmagick, grid, methods, ggtree (>= 1.17.1)
ape, aplot, dplyr, ggplot2 (>= 4.0.0), grid, magrittr,
methods, purrr, rlang, ggfun (>= 0.1.7), yulab.utils (>=
0.1.6), tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0), utils,
scales, stats, cli, ggiraph (>= 0.9.1)
ggplot2 (>= 4.0.0), utils, rlang, ggnewscale, stats, ggtree,
tidytree (>= 0.3.9), cli, magrittr
interp, ape, dplyr, GGally, ggplot2, grid, ggtree, phytools,
rlang, tibble, tidyr, tidyselect, stats
KEGGREST, UniProt.ws, XML, rentrez, httr, utils, memoise,
cachem, jsonlite, rvest
DBI, RMariaDB, RSQLite, numDeriv, RColorBrewer, parallel,
stats, methods, graphics, grDevices, xtable, tools, brew,
stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML
annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM
AnnotationDbi, ape, bnlearn, Category, DT, doParallel,
foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db,
org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics,
reshape2, stats, utils
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)
clusterProfiler, goProfiles, org.Hs.eg.db, parallel, stats,
stringr
AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils
methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>=
1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz
parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS,
stats, utils, grDevices
stats, utils, graphics, ggplot2, plotly, scales, RColorBrewer,
dplyr, grDevices, GenomicRanges, shiny, cowplot, ggpubr,
stringr, rlang
Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats
AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats,
utils, graphics, rlang, lifecycle, purrr, dir.expiry
graphics, grDevices, reshape2, stats, utils
SummarizedExperiment, nloptr, fGarch, methods, BiocParallel,
graphics
dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud,
stringr, gridExtra, rlang, grDevices, graphics, stats, methods
cluster, doParallel, foreach, matchingR, nsga2R, survival,
proxy, stats, methods,
methods, graphics, stats, utils, genefilter, Biobase,
GSEABase, les (>= 1.1.6)
circlize (>= 0.4.8), GetoptLong, grDevices, utils
graphics, stats, utils, methods, gdsfmt, DBI, RSQLite,
GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf,
quantsmooth, data.table
utils, httr2, jsonlite, parallel, filelock, rappdirs
stats, tools, rhdf5filters, S4Vectors, IRanges, S4Arrays
rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>=
2.13.1), methods, GenomicRanges, abind, BiocParallel,
BatchJobs, h5vcData, GenomeInfoDb
utils, stats, tools, Matrix, BiocGenerics (>= 0.51.2),
S4Vectors, IRanges, S4Arrays (>= 1.1.1), rhdf5
dplyr, tidyr, ggplot2, BiocStyle, knitr, methods, grDevices,
stats, MsCoreUtils
methods, grDevices, graphics, stats, Biostrings,
GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage,
RColorBrewer, BiocGenerics, Seqinfo
assertthat, Biobase, BiocGenerics, biomaRt, checkmate (>=
2.1), circlize, ComplexHeatmap, DESeq2, dplyr, edgeR, EnvStats,
forcats (>= 1.0.0), GenomicRanges, ggplot2, ggrepel (>= 0.9),
IRanges, limma, magrittr, matrixStats (>= 1.5.0), methods,
MultiAssayExperiment, purrr, R6, Rdpack (>= 2.6.2), rlang,
S4Vectors, stats, tidyr, utils
matrixStats, stats, data.table, harmonicmeanp, metap, cluster,
spdep, Matrix, limma, methods
Rcpp (>= 1.0.0), RcppEigen(>= 0.3.2.0), Matrix, RANN, ape,
dendextend, ggplot2, mclust, patchwork, dplyr, grDevices,
methods, stats
ggplot2, viridis, RColorBrewer, scales, reshape2, stringr,
data.table, Seqinfo, GenomicRanges, stats, IRanges, grDevices,
S4Vectors, digest, tibble, jsonlite, BiocParallel, R.utils,
readr, methods
data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet,
GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth,
methods, utils, graphics, pheatmap, gtools, rhdf5
methods, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools,
pbapply, BiocParallel, BiocGenerics, grid, cowplot, gridExtra,
data.table, multiHiCcompare, Seqinfo
InteractionSet, strawr, Seqinfo, GenomicRanges, IRanges,
S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5,
Matrix, vroom, dplyr, stats
InteractionSet, SummarizedExperiment, GenomicRanges, IRanges,
GenomeInfoDb, S4Vectors, methods, BiocGenerics, BiocIO,
BiocParallel, RSpectra, Matrix, tibble, tidyr, dplyr, readr,
stringr, ggplot2, ggrastr, scales, stats, utils
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
dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils,
gridExtra
affy, Biobase, gplots, graphics, grDevices, limma, methods,
RColorBrewer, stats, stats4, utils
edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices,
graphics, methods
httr2, dplyr, tidyr, tibble, rjsoncons, utils, stringr,
whisker, purrr, rlang
available, usethis, biocthis, dplyr, aws.s3, fs, BiocManager,
utils
Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges
ggplot2, patchwork, rlang, DESeq2, SummarizedExperiment,
stats, methods, RColorBrewer, ComplexHeatmap, grDevices,
BiocParallel
methods, grid, graph, hypergraph, Rgraphviz, stats4
irlba, stats, cluster, graphics, SummarizedExperiment,
BiocParallel
fields, ggplot2, truncnorm, tidyr, data.table, dplyr,
grDevices, graphics, stats, utils, rlang
shiny (>= 0.9.1.9008), shinydashboard, shinyBS, reshape2,
ggplot2 (>= 3.4.0), scales, ROCR, dplyr, DT, limma, methods,
UpSetR, utils, rlang
dplyr (>= 0.7.6), futile.logger (>= 1.4.3), GenomeInfoDb (>=
1.14.0), GenomicRanges (>= 1.30), ggplot2 (>= 3.1.1),
grDevices, grid, idr (>= 1.2), IRanges (>= 2.18.0), magrittr
(>= 1.5), methods, reticulate (>= 1.13), scales (>= 1.0.0),
stats, stringr (>= 1.3.1), utils
mathjaxr, doRNG, foreach (>= 1.4.3), Matrix (>= 1.4-0), HDCI
(>= 1.0-2), parallel (>= 3.3.0), doParallel (>= 1.0.11),
parallelly , glmnet, stats, utils, SummarizedExperiment,
stringr, S4Vectors, DescTools, MatrixExtra, methods
methods, utils, stats, tools, R.utils, curl, httr, xml2,
rvest, xtable, jsonlite, S4Vectors, IRanges, GenomeInfoDb
methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel
(>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0),
SummarizedExperiment, tidyr
BiocGenerics, checkmate, futile.logger, GenomeInfoDbData,
htmlwidgets, httr, jsonlite, randomcoloR, utils
methods, slam, lpsymphony, fdrtool, BiocGenerics
DT, dplyr, bslib, bsicons, ggplot2, viridis, tidyr, leaflet,
clipr, rlang
STRINGdb, pwalign, igraph, graphics, utils, seqinr
methods, stats, graphics, grid, lattice, grDevices
ggplot2, httr, jsonlite, patchwork, UniProt.ws
stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr,
xml2, maps, rlang
config (>= 0.3.2), golem (>= 0.4.1), shiny (>= 1.7.5),
ComplexHeatmap, DT, RColorBrewer, WGCNA, corrplot, cowplot,
dynamicTreeCut, ggplot2, glassoFast, impute, purrr, stringr,
tidyr, visNetwork, shinyBS, httr, dplyr, stats, iModMixData,
SummarizedExperiment, ExperimentHub (>= 2.99.0)
stats, grDevices, utils, graphics, pbapply, matlab, png,
raster, grid, uwot, gtools, Biobase, generics, parallel,
methods, xgboost
SQUAREM, bdsmatrix, numDeriv, stats, tidyr, ggplot2
methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.27.12),
IRanges, Seqinfo
grDevices, stats, shiny, grid, GetoptLong, S4Vectors (>=
0.26.1), digest, IRanges, kableExtra (>= 1.3.1), utils,
svglite, htmltools, clisymbols, jsonlite, RColorBrewer,
fontawesome
config, golem, shiny, DT, shinydashboard, shinyFiles,
shinycssloaders, data.table, fs, dplyr, tidyr, circlize,
colourpicker, dendextend, factoextra, ggplot2, plotly, plyr,
shinyFeedback, shinyalert, tibble, umap, visNetwork,
wordcloud2, readxl, htmlwidgets, colorspace, signal, scales,
htmltools, ComplexHeatmap, grDevices, stats, tools, utils,
biomaRt, rlang, fmsb, igraph
igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats,
utils, grDevices, graphics
rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2,
methods, BiocGenerics, XVector, tibble, stats, BiocParallel,
bit64, stringr, utils
Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats,
assertthat
utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs,
lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools,
grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib,
vegan, data.table, DT
Rcpp, Matrix, data.table, methods, pbapply, parallelly,
stringfish,
methods, Rcpp, data.table, glue, stats, doParallel, parallel,
doRNG, foreach, iterators, ggplot2, HDInterval,
SummarizedExperiment, S4Vectors
dplyr, magrittr, methods, quadprog, readr, readxl, stringr,
tibble, tools, utils, pracma, WriteXLS
IsoCorrectoR, readxl, tcltk2, tcltk, utils
affxparser, DBI, GLAD, oligo, oligoClasses, stats
graphics, grDevices, stats, survival, utils
shiny, survival, survminer, hwriter, plotly, ggplot2,
S4Vectors, graphics, stats, utils, UpSetR
methods, stats, Rcpp (>= 0.11.2), Matrix (>= 1.5-0), XVector
(>= 0.7.3), S4Vectors (>= 0.27.3), e1071, LiblineaR, graphics,
grDevices, utils, apcluster
methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz
AnnotationDbi, DBI, grDevices, methods, tools, utils
data.table, BiocParallel, sqldf, stats, grid, grDevices
survival, tools, methods, pracma, doParallel, foreach,
parallel, SummarizedExperiment, S4Vectors
stringr, methods, ggplot2 (>= 3.3.0), jsonlite, kernlab,
rlist, rmarkdown, reshape2, e1071, randomForest, caret, XML,
praznik, R.utils, httr, sva (>= 3.30.1), edgeR (>= 3.24.3),
limma (>= 3.38.3), grDevices, graphics, stats, utils, Hmisc (>=
4.4.0), gridExtra
sesameData, dplyr, methods, rlang, GenomicRanges, IRanges,
reshape2, S4Vectors, stats, stringr, utils, ggplot2, ggrepel,
tibble, wheatmap, magrittr
curl, igraph, foreach, doParallel, sortable, dplyr, forcats,
data.tree, graphics, grDevices, parallel, RColorBrewer, Rfast,
stats, SummarizedExperiment, utils, purrr, stringi, stringr,
Matrix, tidyr, jsonlite, readr, configr, DT, tools, fs,
data.table, htmltools, htmlwidgets, bsplus, shinyvalidate,
shiny, shinythemes, shinyFiles, shinyjs, shinyBS,
shinydashboard, biomaRt, callr, logr, ggplot2, svglite
BiocGenerics (>= 0.25.1), Seqinfo, httr, Matrix
akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl,
ROCR, testthat
Hmisc, stats, energy, grDevices, graphics, utils,
MultiAssayExperiment, ggplot2, ggpubr
grDevices, graphics, stats, utils, methods, statmod
methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot,
xtable, utils
ggplot2, stringr, plyr, ggrepel, reshape2, grDevices,
graphics, doParallel, parallel, dplyr, tibble, tidyr, ggsci,
tidyverse, methods, stats, SummarizedExperiment, S4Vectors
limma, stringr, qvalue, utils, stats, BiocParallel, S4Vectors,
dplyr
scales, cluster, graphics, ggpubr, gridExtra, vegan, rio,
MultiAssayExperiment, emmeans, reshape2, data.table
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
dplyr, ggnewscale, ggplot2, magrittr, methods, rlang,
SummarizedExperiment, MKmisc, matrixTests
Biobase, graphics, grDevices, methods, stats
pheatmap, wordcloud, RColorBrewer, data.table, methods,
grDevices, stats, graphics, GenomicRanges, BiocParallel,
S4Vectors
methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase
BiocParallel, dplyr, ggplot2, ggrepel, magrittr, stats, utils
data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
RColorBrewer, circlize, grid, utils, stats, ggtree, msa,
Biostrings, phangorn, stringdist, UpSetR
ggplot2, Matrix, doSNOW, cluster, parallel, foreach,
doParallel, matrixcalc, Rtsne, corpcor, umap
readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel,
methods, stats, latticeExtra, lattice, rmarkdown, png, grid,
gridExtra, prettydoc, rvest, xml2
utils, reticulate, S4Vectors, methods, basilisk,
ExperimentHub, AnnotationHub
data.table, grDevices, methods, RColorBrewer, Rhtslib,
survival, DNAcopy, pheatmap
caret, parallel, doParallel, foreach, e1071, future.apply,
future, missForest, pcaMethods, tidyverse, stats, utils,
methods, SummarizedExperiment, S4Vectors
flowCore, Biobase, stringr, uwot, iCellR, igraph, ggplot2,
RColorBrewer, Rfast, ComplexHeatmap, circlize, glmnetUtils,
e1071, xgboost, parallel, pbapply, reshape2, gtools, utils,
stats, cowplot, methods, grDevices, graphics
circlize, edgeR, ComplexHeatmap, ggh4x, ggplot2, ggpubr, grid,
gridExtra, pROC, RColorBrewer, reshape2, rstatix, scales,
stats, utils, fgsea, limma, ggrepel, effectsize, msigdbr,
tibble
Rcpp, SummarizedExperiment, utils, methods, ggplot2, dplyr,
magrittr, rlang, S4Vectors
Biobase, graphics, grDevices, venn, mclust, stats, MASS
BiocGenerics, ProtGenerics, digest, irlba, stats, stats4,
graphics, grDevices, parallel, utils
methods, magrittr, phyloseq, limma, lme4, lmerTest, pheatmap,
rmarkdown, cluster, dplyr, ggplot2, gridExtra, ruv, sva,
tibble, tidyr, vegan, stats, utils, Matrix
Biobase, graphics, methods, utils, grDevices
stats, graphics, utils, limma (>= 3.30.13),
SummarizedExperiment (>= 1.10.0), preprocessCore (>= 1.36.0),
BiocFileCache, rappdirs, xml2, RCurl, ggplot2, PairedData,
rmarkdown
BiocParallel, graphics, utils, stats, AnnotationDbi, GO.db,
org.Hs.eg.db, GGally, ggplot2, scales, cluster, WGCNA
GenomicAlignments, GenomicRanges, IRanges, Biostrings,
DNAcopy, Rsamtools, parallel, stringr
xfun, utils, fs, GenomicRanges, readr, cmdfun, dplyr, magrittr
Biostrings, dplyr, cmdfun (>= 1.0.2), GenomicRanges, ggplot2,
ggseqlogo, magrittr, matrixStats, methods, patchwork, processx,
purrr, rlang, readr, stats, tools, tibble, tidyr, utils,
usethis, universalmotif (>= 1.9.3), xml2
methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase
AnnotationDbi, DOSE, enrichplot, GOSemSim (>= 2.31.2),
methods, utils, AnnotationHub, MeSHDbi, yulab.utils (>= 0.1.5)
markdown, rmarkdown, BiocStyle, knitr, methods, stats, utils,
fdrtool, MeSHDbi, Category, S4Vectors, BiocGenerics, RSQLite
methods, data.table, Biostrings, dplyr, tidyr (>= 1.0.0), ape
(>= 5.4.1), ggrepel, pracma, ggridges, AnnotationDbi, IRanges,
circlize, cowplot, mclust, phangorn, ComplexHeatmap (>= 1.9.3),
ggplot2, RColorBrewer, grDevices, stats, utils, S4Vectors
dplyr (>= 1.0), methods, mgcv, caret, S4Vectors, stats, utils,
rlang, graphics, matrixStats, tidyr
BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics,
methods, S4Vectors, Spectra (>= 1.17.6), BiocParallel,
SummarizedExperiment, QFeatures, AnnotationHub, graphics,
CompoundDb
utils, MsCoreUtils, BiocParallel, methods, stats
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, rlang, ape, ggtree, patchwork
optimx, Formula, plyr, multtest, BiocParallel, ggplot2
flowCore (>= 1.4),tidyr (>=
0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices,
graphics, stats, utils
stats, RANN, igraph, vegan, edgeR, ecodist, ggplot2, viridis,
ggpubr, ape, cluster, matrixStats
Matrix, tools, robustbase, BiocGenerics, graphics, stats,
utils
utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats,
clusterProfiler, RecordLinkage, RCy3
Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats,
GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm,
data.table
BiocParallel, parallel, stats, methods, corpcor,
SummarizedExperiment, utils
foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute,
data.table, limma, R.matlab, digest
shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings,
pwalign, Rfast, grDevices, graphics, stats, utils, tools,
methods, shinyFiles, data.table, SummarizedExperiment
Biostrings, compositions, dplyr, reshape2, Rtsne, scales,
stats, tibble, tidyr, utils, vegan
clusterProfiler (>= 4.5.2), config, DT, enrichplot, golem,
gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets,
shinycustomloader, htmltools, ggplot2, graphics, stats, utils,
yulab.utils
ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel,
vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang,
tibble, grDevices, stats, utils, coin, ggsignif, patchwork,
ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>=
1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table,
ggfun (>= 0.1.1)
TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2,
ggpubr, ggridges, glue, S4Vectors, dirmult
BiocGenerics, S4Vectors, preprocessCore, grDevices, methods,
grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses
methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory,
foreach, ggplot2, parallel, parallelDist, reshape2, plyr,
biganalytics, stringr, Hmisc, utils
methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>=
0.23.18), IRanges, Seqinfo, GenomicRanges (>= 1.17.16),
SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff,
foreach, matrixStats, lattice, data.table, grid, stats, utils
utils, methods, graphics, KernSmooth, stats
graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi,
Rgraphviz
methods, stats, utils, RCurl, httr, stringr, Hmisc, energy,
entropy, gplots, glmnet, impute, limma,
pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc,
InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db
DBI, RSQLite, stringr, sqldf, plyr, methods
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
purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap,
reshape2, corrplot, grDevices, graphics, stats, utils,
data.table, R.utils, viridis
assertthat, caret, deldir, digest, distances, dplyr (>=
1.1.0), filelock, furrr (>= 0.2.0), ggplot2, methods, purrr,
ranger, readr (>= 2.0.0), ridge, rlang, rlist, R.utils, stats,
stringr, tibble, tidyr, tidyselect (>= 1.2.0), utils, withr
stats, grDevices, graphics, utils, MASS, plyr, reshape2,
parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2,
gplots, beeswarm, echarts4r, kableExtra, dplyr, network
AnnotationDbi, ape, circlize, clusterProfiler, ComplexHeatmap,
ggplot2, ggtree, magrittr, org.Hs.eg.db, ReactomePA, scales
igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr,
tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra,
grDevices, graphics, stats, ggrepel, BiocParallel, utils,
gsignal, rgl
gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis,
shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench,
stats4, tools, grDevices, graphics, stats, magrittr,
SummarizedExperiment
AnnotationDbi, gplots, graphics, stats, utils
testthat, VennDiagram, pamr, methods, DESeq2, edgeR, limma,
Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq,
xtable
cluster, graph, Rgraphviz, flexclust, lattice, naturalsort,
snowfall, stats4, tsne, methods, graphics, stats, utils,
Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices,
e1071, ggplot2, wesanderson
S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics,
methods, grDevices, reshape2, NMI, zoo, ClusterR, splines,
matrixStats
grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut,
igraph, cluster, AMOUNTAIN, RColorBrewer
methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges,
XVector, stringi, stringr, crayon, grDevices
rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods,
RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array,
grDevices, stats, magrittr, forcats, utils, corrplot,
DelayedArray, Rtsne, uwot, basilisk, stringi
stats, utils, RCy3, stringr, graphics, grDevices, RUnit,
BiocParallel, igraph
methods, graphite, genefilter, BiocGenerics, gplots, GSEABase,
Biobase, parallel, corpcor, svd, cluster, grDevices, graphics,
stats, utils
circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics,
grid, grDevices, magrittr, methods, MKmisc,
MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr,
reshape2, rlang, stats, stringr, tibble, tidyr, utils
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)
parmigene, randomForest, SummarizedExperiment, gplots,
circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase,
limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats,
RISmed, grid, utils
MASS, splines, lattice, IRanges, GenomicRanges,
GenomicAlignments, Rsamtools, Seqinfo, S4Vectors
Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust,
isa2, QUBIC, akmbiclust, RColorBrewer
Seqinfo, graphics, harmonicmeanp, IRanges, matrixStats,
methods, parallel, patchwork, rlang, S4Vectors, stats,
universalmotif,
httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales,
gtools, tidyr, data.table, jsonlite, rlist, Seqinfo, methods,
biomaRt, stats, IRanges
S4Vectors, scales, stats, graphics, statmod
BiocParallel, methods, progress, stats, SummarizedExperiment
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
BiocParallel, S4Vectors, IRanges, methods, ProtGenerics (>=
1.35.3), MsCoreUtils, DBI, utils
curl, ProtGenerics, BiocFileCache, S4Vectors, methods,
progress
ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges,
MsCoreUtils, methods, stats
ProtGenerics (>= 1.35.3), MsCoreUtils, S4Vectors, IRanges,
rawrr (>= 1.17.2), utils, BiocParallel
BiocParallel, S4Vectors, methods, ProtGenerics (>= 1.35.3),
DBI, MsCoreUtils, IRanges, data.table, progress, stringi,
fastmatch, BiocGenerics
methods, S4Vectors, IRanges, Spectra, SummarizedExperiment,
QFeatures, DBI, BiocGenerics
methods, ProtGenerics (>= 1.23.5), MsCoreUtils,
SummarizedExperiment, stats
data.table (>= 1.13.0), doRNG, fmsb, foreach, magrittr,
org.Hs.eg.db, pROC, randomForest, RankProd, stats, utils
MsCoreUtils, PSMatch (>= 1.13.2), 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
MSnbase (>= 1.12.1), mzID (>= 1.3.5), R.cache, foreach,
doParallel, parallel, methods, iterators, data.table, Biobase,
ProtGenerics, reshape2, dplyr, mzR, BiocStyle, msmsTests,
ggplot2, RUnit, BiocGenerics, Biostrings, purrr, rlang,
stringr, tibble, AnnotationHub, AnnotationDbi, xtable
QFeatures, limma, SummarizedExperiment, magrittr, rlang,
dplyr, purrr, stats, tidyr, stringr, ggplot2, ggseqlogo,
heatmaply, readr, rstatix, tibble, ggpubr
plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW,
stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite
stats, methods, lme4, purrr, BiocParallel, Matrix, MASS,
limma, SummarizedExperiment, MultiAssayExperiment, codetools
MSstatsConvert, data.table, checkmate, MASS, htmltools, limma,
lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel,
gplots, plotly, marray, stats, grDevices, graphics, methods,
statmod, parallel, rlang
arrow, DBI, dplyr, MSstats, MSstatsConvert, readr, sparklyr,
utils
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
minpack.lm, ggplot2, utils, stats, grDevices
dplyr, gridExtra, stringr, stats, ggplot2, stringi, grDevices,
MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp,
Biostrings, checkmate, ggrepel, plotly, htmltools
shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid
BiocParallel, ggplot2, dplyr, stats, parallel, data.table
shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2, plotly,
data.table, Hmisc, MSstats, MSstatsTMT, MSstatsPTM,
MSstatsConvert, gplots, marray, DT, readxl, ggrepel, uuid,
utils, stats, htmltools, methods, tidyr, grDevices, graphics,
mockery, MSstatsBioNet, shinydashboard, arrow, tools
limma, lme4, lmerTest, methods, data.table, stats, utils,
ggplot2, grDevices, graphics, MSstats, MSstatsConvert,
checkmate, plotly, htmltools
graphics, grDevices, stats, methods, fields
Biobase, BiocBaseUtils, BiocGenerics, DelayedArray,
GenomicRanges, IRanges, MatrixGenerics, methods, S4Vectors,
tidyr, utils
mclust, ctc, survival, cluster, dendextend, amap, graphics,
grDevices
magrittr, graphite, AnnotationDbi, metaboliteIDmapping, dplyr,
fgsea, metap, rappdirs, rlang, methods
data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman,
pheatmap, methods, GenomicRanges, graphics, stats, utils,
pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation
stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 2.0), methods,
BiocGenerics, AnnotationDbi, dplyr,
methods, S4Vectors, data.table, grid, dplyr, tidyr,
matrixStats, stats, fitdistrplus, viridis, ggplot2, circlize,
mashr, grDevices
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
glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra,
igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST,
ComplexHeatmap, stats, utils
XML, plyr, parallel, doParallel, foreach, iterators,
ProtGenerics
Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3),
ncdf4
BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes,
grDevices, IRanges, methods, pheatmap, RColorBrewer, stats,
utils
DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods,
stats,
graph, KEGGgraph, methods, RBGL, RCy3, R.oo
httr, xml2, utils, methods, grDevices, ggplot2, IRanges,
GenomicRanges, S4Vectors
e1071, nnet, randomForest, naturalsort, graphics, stats,
utils, matrixStats, epiNEM
airway, DelayedArray, DelayedMatrixStats, DESeq2, methods,
methods, NetActivityData, SummarizedExperiment, utils
Rcpp, RcppParallel, parallel, grDevices, graphics, stats,
utils, dynamicTreeCut, WGCNA, impute, colorspace, methods,
BiocStyle, R.utils
glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust,
parallel, GSA, limma, multtest, ICSNP, glmnet, network,
ggplot2, grDevices, graphics, stats, utils
stats, Matrix, dplyr, doParallel, foreach, parallel,
sparseMVN, ggplot2, gridExtra, pROC
ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer
Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro,
grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate,
methods, plotly (>= 4.9.4), rlang, rmarkdown, scales, stats,
stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo
ComplexHeatmap, dplyr, fgsea, ggplot2 (>= 3.0.0), graphics,
grid, methods, MultiAssayExperiment, SummarizedExperiment,
pracma, rlang, RSpectra, scales, stats
graphics, grDevices, marray, methods, nnet, stats
limma, mvtnorm, utils, methods, arm, HTqPCR (>= 1.16.0)
vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods,
utils, stats, SummarizedExperiment, matrixStats, ggforce
BiocGenerics, BiocParallel, dplyr, futile.logger, methods,
openxlsx, S4Vectors, scales, stringr, tidyr, utils
BiocGenerics, cowplot, devEMF, dplyr, ggbeeswarm, ggdendro,
ggrepel, grDevices, methods, notame, scales, stringr, stats,
tibble, tidyr, utils
dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr,
stats, methods
Biobase, methods, BiocGenerics, graphics, stats
stats, IRanges, S4Vectors, graphics, methods
Biobase, BiocGenerics, Biostrings, Seqinfo, GenomicRanges,
IRanges, Rsamtools, S4Vectors, ShortRead, dplyr, ggplot2,
magrittr, parallel, stats, utils, grDevices
multtest (>= 1.7.3), graphics, grDevices, stats, interp
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
BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods,
graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7),
SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>=
1.23.2), foreach, BiocManager, utils, S4Vectors (>= 0.9.25),
RSQLite, DBI, ff
graphics, grDevices, limma, marray, methods, stats
graphics, marray, OLIN, tcltk, tkWidgets, widgetTools
utils, ape, Biostrings, GenomicRanges, IRanges, methods,
topGO, jsonlite
compositions, DT, grDevices, knitr, jsonlite, matrixStats,
rmarkdown, shiny, stats, vegan, zCompositions
methods, matrixStats, graphics, stats, SummarizedExperiment,
MultiAssayExperiment, RaggedExperiment
survminer, survival, fastmatch, reshape2, stringr, beeswarm,
grDevices, DT, shiny, shinythemes, shinyWidgets, plotly,
networkD3, httr, matrixStats, RColorBrewer, Biobase, fgsea,
openxlsx, psych, shinybusy, ggseqlogo, htmlwidgets, graphics,
grid, stats, utils, methods, shinyjs, curl, flatxml, ggplot2,
S4Vectors, SummarizedExperiment, RSQLite, Matrix,
shinycssloaders, ROCR, drc
dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr,
tidyselect, grid, stats, stringr
ggplot2, ggrepel, RColorBrewer, mclust, stats,
SummarizedExperiment
biomaRt, grDevices, graphics, utils, methods,
Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz,
gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr,
smatr, ggplot2, ggrepel, stringr
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
MASS, jsonlite, Hmisc, methods, knitr, AICcmodavg, car, rlist,
summarytools, graphics, stats, utils
fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt,
Biobase, RcppParallel, Rcpp, methods, graph, XML, png, RCurl
transport, parallel, Rfast, robustbase, dbscan, randomForest,
foreach, graphics, doParallel, stats, flowMeans, rgl, ellipse
dplyr, methods, stats, utils, Matrix, jsonlite, homologene,
gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr,
patchwork, DelayedArray, grr, repmis, ggtree, tools
AnnotationHub, basilisk, BiocParallel, colorspace, cowplot,
DelayedArray, dplyr, ExperimentHub, ggplot2 (>= 3.4.0), ggpubr,
ggrepel, ggsci, grDevices, grid, HDF5Array, keras (>= 2.16.0),
methods, orthosData, parallel, plyr, reticulate, rlang,
S4Vectors, stats, tensorflow, tidyr
stats, utils, methods, BiocParallel, SummarizedExperiment,
limma, fdrtool, Rcpp
e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR,
sva
Biostrings, GenomicRanges, kmer, ape, methods, IRanges,
S4Vectors
FactoMineR, MultiAssayExperiment, methods, graphics, stats,
utils
limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db,
hgu133a.db, KEGGREST, nlme
SummarizedExperiment, S4Vectors, stats, methods, abind,
BiocParallel
DESeq2, DEXSeq, limma, fgsea, msigdbr, sva,
SummarizedExperiment, S4Vectors, BiocParallel, ggplot2,
aggregation, stats, utils, methods, showtext
SummarizedExperiment, KEGGREST, igraph, data.table, methods,
stats, magrittr, CompQuadForm, tibble
matrixStats, igraph, ggplot2, grid, reshape, plyr, RUnit,
hexbin
GenomicRanges, Rsamtools, IRanges, S4Vectors, Seqinfo,
grDevices
clusterProfiler, dplyr, forcats, GSEABase, igraph, limma,
metap, org.Hs.eg.db, parallel, preprocessCore, RColorBrewer,
rlang, tibble, withr, utils
graphics, grDevices, MASS, methods, pvclust, stats, utils,
RedeR
circlize, clusterProfiler, ComplexHeatmap, dplyr, fgsea,
ggforce, ggplot2, ggpubr, ggraph, ggrepel, grid, igraph, purrr,
sigora, stringr, tibble, tidygraph, tidyr, vegan, visNetwork
limma, corpcor,matrixStats, reshape2, scales, ggplot2,
rentrez, DT, tidyr, plyr, dplyr, phyloseq, shiny, stats,
methods, XML, graphics, utils, BiocStyle, edgeR, DESeq2,
ComplexHeatmap, plotly, webshot, vegan, shinyjs, glmnet,
gmodels, ROCR, RColorBrewer, knitr, devtools, ape
KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi,
org.Hs.eg.db, KEGGREST, methods, utils
lars, methods, parallel, stats, survival, utils
data.table, MultiAssayExperiment, ConsensusClusterPlus,
igraph, ggplotify, matrixStats, RColorBrewer, clusterRepro,
CoreGx, caret, survminer, methods, S4Vectors, BiocGenerics,
survival, stats, plyr, dplyr, MatrixGenerics, BiocParallel,
rlang, piano, scales, survcomp, genefu, ggplot2, switchBox,
reportROC, pROC, verification, utils
circlize, ComplexHeatmap, flowCore, flowWorkspace, ggplot2,
grDevices, grid, gridExtra, methods, plyr, stats, utils
tidyr, dplyr (>= 1.1.2), IRanges, GenomicRanges, tidyselect,
purrr, readr (>= 2.1.2), tibble (>= 3.2.1), rlang, stringr,
here, stats, Seqinfo
ROTS, limma, affy, genefilter, preprocessCore,
aroma.affymetrix, aroma.core
graphics, stats, methods, ggplot2, utils, grDevices, stringr,
plyr, dplyr, tidyr, quadprog, Matrix, S4Vectors, shiny, readxl,
DT, igraph, shinycssloaders, shinyhelper, shinyjs, shinyjqui,
shinyWidgets, htmlwidgets, plotly, colourpicker, shinytoastr
dplyr, limma, lme4, MASS, matrixStats, reshape2, stats,
tibble, SummarizedExperiment, methods
Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2,
methods, graphics, stats
limma, fields, GenomicRanges, ggplot2, plyr, tools, methods,
data.table
utils, methods, grDevices, graphics, circlize, httr, dplyr,
attempt, lubridate, survival, survminer, ggplot2,
GenomicRanges, SummarizedExperiment, S4Vectors, yaml, parallel,
future, future.apply
ggplot2, protolite, Biobase, GEOquery, Rook, htmltools,
httpuv, jsonlite, limma, edgeR, opencpu, assertthat, methods,
httr, rhdf5, utils, parallel, stringr, fgsea (>= 1.9.4),
svglite, gtable, stats, Matrix, pheatmap, scales, ccaPP, grid,
grDevices, AnnotationDbi, DESeq2, data.table, curl, apeglm,
tidyr, config (>= 0.3.2), rhdf5client (>= 1.25.1), yaml, fs,
phantasusLite, XML
data.table, rhdf5client(>= 1.25.1), httr, stringr, stats,
utils, Biobase, methods
BiocGenerics, Biobase, S4Vectors, SummarizedExperiment,
MultiAssayExperiment, BiocParallel, ggplot2, RColorBrewer,
magicaxis, parallel, caTools, methods, downloader, stats,
utils, graphics, grDevices, reshape2, jsonlite, data.table,
checkmate, boot, coop
igraph, Matrix, foreach, doParallel, dplyr, stats, utils,
parallel
Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr,
tibble, ggplot2, tidyr
survival, limma, gplots, Category, AnnotationDbi, hopach,
biomaRt, GSEABase, genefilter, xtable, annotate, mgcv,
hgu133a.db, ellipse
ape, phangorn, tidyr, ggplot2, ggtree, methods
BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges,
S4Vectors, edgeR, cli, utils
plyr, stats, graphics, matrixStats, methods
ruv, e1071, dendextend, limma, pcaMethods, stats,
RColorBrewer, circlize, dplyr, igraph, pheatmap,
preprocessCore, tidyr, rlang, graphics, grDevices, utils,
SummarizedExperiment, methods, S4Vectors, BiocGenerics,
ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext,
stringi
ape, bioDist, BiocStyle, Biostrings, bsplus, colourpicker,
data.table, dplyr, DT, energy, fastcluster, ggplot2, gridExtra,
htmlwidgets, pbapply, plotly, RColorBrewer, RCurl, Rfast,
scattermore, shiny, shinycssloaders, shinyFiles, shinyjs,
stringr, tsne, svglite, umap, xml2, zoo, yaml
BiocGenerics, Biobase, gplots, igraph, relations, marray,
fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard,
visNetwork, scales, grDevices, graphics, stats, utils, methods
utils, Seqinfo, GenomicRanges, GenomicAlignments, Biostrings,
Rsamtools, data.table, IRanges, seqinr, stats, openxlsx, dplyr,
S4Vectors, methods
dplyr, utils, stats, GenomicRanges, BiocGenerics, methods
utils, Biobase (>= 2.5.5), MASS, methods
dplyr, purrr, rlang, SummarizedExperiment, tidyr, tidyselect,
vctrs, tibble, pillar, cli, glue, S7, S4Vectors, utils, methods
ggplot2, gridExtra, mclust, diptest, rlist, shiny, DT,
LaplacesDemon, purrr, shinyjs, readr, grDevices, stats, utils
stats, utils, grDevices, mvtnorm, sn, dplyr, flowPeaks,
ggplot2, tidyverse, cowplot, mlrMBO, DiceKriging, smoof,
ParamHelpers, lhs, rgenoud, BiocManager
broom, caret, ComplexHeatmap, dbscan, dplyr, DESeq2, fgsea,
FSA, ggcorrplot, ggplot2, ggrepel, glmnet, grid, impute,
janitor, limma, lme4, magrittr, MASS, mixOmics, multcomp,
msigdbr, purrr, randomForest, RankProd (>= 3.14), rlang,
SummarizedExperiment, sva, tibble, tidyr, utils, uwot, vegan
cubature, doParallel, evmix, foreach, magrittr, methods,
parallel, purrr, stats, truncdist, vegan, VGAM
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
parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges,
Biobase, Seqinfo, S4Vectors
graphics, grDevices, Icens, stats, utils
methods, stats, graphics, S4Vectors, Biostrings, utils
Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra,
decoupleR, reshape2
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, colorspace
shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics,
utils, ggplot2, shinydashboardPlus (>= 2.0.0), colourpicker,
shinyhelper, shinyWidgets, shinyjs, colorspace, stats,
grDevices, grid, BiocGenerics, shinydashboard
dplyr, magrittr, data.table, RColorBrewer, ggplot2, S4Vectors,
ComplexHeatmap, stringr, NormalyzerDE, tibble, limma, MASS,
edgeR, matrixStats, preprocessCore, stats, gtools, methods,
ROTS, ComplexUpset, tidyr, purrr, circlize, gprofiler2,
plotROC, MSnbase, UpSetR, dendsort, vsn, Biobase, reshape2,
POMA, ggtext, scales, DEqMS, vegan
bnlearn, reshape2, sva, stats, utils, Biobase
DAPAR (>= 1.35.1), DAPARdata (>= 1.30.0), rhandsontable,
data.table, shiny, shinyBS, shinyAce, highcharter, htmlwidgets,
webshot, shinythemes, later, shinycssloaders, future, promises,
shinyjqui, tibble, ggplot2, gplots, shinyjs, vioplot, Biobase,
DT, R.utils, RColorBrewer, XML, colourpicker, gtools, markdown,
rclipboard, sass, shinyTree, shinyWidgets
gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats,
graphics
utils, stats, igraph, methods, Spectra (>= 1.17.10), Matrix,
BiocParallel, BiocGenerics, ProtGenerics (>= 1.27.1),
QFeatures, MsCoreUtils, IRanges
Biobase, bit64, chron, data.table, doParallel, DT, enviPat,
foreach, ggplot2, graphics, grDevices, ggpubr, gridExtra,
Hmisc, methods, minpack.lm, MSnbase, parallel, plotly, rhdf5,
rlang, Rcpp, shiny, shinyscreenshot, signal, scales, stats,
utils
Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses
Biobase, methods, knitr, tools, xtable, pander, S4Vectors
graphics, methods, stats, utils, BiocGenerics, Biobase (>=
2.18.0), CGHbase (>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>=
1.32.0), Seqinfo, GenomicRanges (>= 1.20), IRanges (>= 2.2),
matrixStats (>= 0.60.0), R.utils (>= 2.9.0), Rsamtools (>=
1.20), future.apply (>= 1.8.1)
methods, stats, utils, S4Vectors, IRanges,
SummarizedExperiment, BiocGenerics (>= 0.53.4), ProtGenerics
(>= 1.35.1), AnnotationFilter, lazyeval, Biobase, MsCoreUtils
(>= 1.7.2), igraph, grDevices, plotly, tidyr, tidyselect,
reshape2
rlang, ggplot2, patchwork, heatmaply, methods, MsCoreUtils,
stats, igraph, VIM, scales, grDevices, graphics, limma
MASS, pscl, arrangements, hitandrun, assertthat, dplyr,
BiocParallel
SummarizedExperiment, utils, sva, stats, methods, graphics,
Hmisc
dplyr, sva, stats, ggplot2, rlang, methods
methods, rlang, checkmate, dplyr, collapse, vroom, tidyr,
tibble, utils, stats, ashr, S4Vectors, BiocGenerics
Biobase, limSolve, MASS, methods, preprocessCore, stats,
SummarizedExperiment, ggplot2, tidyr, rlang, utils
SummarizedExperiment, BiocGenerics, data.table, S4Vectors,
Biobase, parallel, BiocParallel, RColorBrewer, caTools,
magicaxis, methods, reshape2, scales, grDevices, graphics,
stats, utils, assertthat, matrixStats, downloader
BiocBaseUtils, BiocGenerics, Seqinfo, IRanges, Matrix,
MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment
(>= 1.39.1), utils
methods, data.table, Seqinfo, GenomicRanges, IRanges,
BiocGenerics, S4Vectors, Rcpp
graphics, stats, utils, digest, glmnet, KernSmooth, grDevices,
GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings,
BiocGenerics
methods, graphics, utils, stats, Rdpack (>= 0.7)
curl, jsonlite, methods, paws.storage, R.utils, utils
dplyr, ggplot2 (>= 3.4), grDevices, hexbin, htmltools,
BiocManager, BiocParallel, rawrr (>= 1.15.5), rlang, reshape2,
scales, shiny (>= 1.5), stats, utils
Rcpp (>= 1.0.6), dada2, ggplot2, readr, doParallel, foreach,
grDevices, stats, utils
EBImage, methods, rJava (>= 0.9-6), S4Vectors, stats
stringr, gplots, ggplot2, methods, stats, utils, shiny
RColorBrewer, alabama, edgeR, reshape2, tseries, stats, VGAM,
ggplot2 (>= 2.2.1.9000), nleqslv, phyloseq, tensor, MASS,
grDevices, graphics, methods
Biostrings, GOSemSim, curl, doParallel, foreach, httr2,
jsonlite, methods, rlang, stats, utils
utils, stats, BiocParallel, batchtools, DiagrammeR, shiny,
R.utils, codetools, basilisk
rappdirs, methods, utils, git2r, httr, S4Vectors
httr, methods, RJSONIO, XML, utils, BiocGenerics, stats,
graph, fs, uuid, stringi, glue, RCurl, base64url, base64enc,
IRkernel, IRdisplay, RColorBrewer, gplots
methods, httpuv (>= 1.5.0), BiocGenerics, base64enc, utils
graphics, grDevices, methods, stats, MASS, rgl
AnnotationDbi, DOSE (>= 3.5.1), enrichplot, ggplot2 (>=
3.3.5), ggraph, reactome.db, igraph, graphite, gson,
yulab.utils (>= 0.1.5)
utils, methods, knitr (>= 1.32), rmarkdown, CodeDepends,
dir.expiry, filelock, BiocStyle
phyloseq, ks, reshape2, ggplot2, stats, methods, graphics,
grDevices, matrixStats, Matrix
WGCNA, ica, moments, clusterProfiler, msigdbr, RColorBrewer,
car, lme4, lmerTest, pheatmap, biomaRt, stats, grDevices,
BiocParallel, ggplot2, patchwork, BiocGenerics, S4Vectors
randomForest, fgsea, DOSE, BiocParallel, DESeq2, limma, WGCNA,
ggplot2 (>= 2.2.0), methods, reshape2, magrittr, BiocStyle
glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats,
pbapply, utils, methods
Rcwl, RcwlPipelines, BiocFileCache, S4Vectors, stats, tools,
utils, methods, jsonlite, yaml, basilisk
methods, utils, stats, lsr, FactoMineR, stringr, circlize,
corrplot, ggplot2, ggridges, reshape2, pryr, S4Vectors,
imputeLCMD, scatterplot3d, glmnet, gridExtra, grid, Hmisc,
gplots, gtools, scales, lme4, grDevices, graphics, ggrepel,
mice
httr, stringi, rsvg, magick, data.table, Biostrings, utils,
rvest, xml2, IRanges, S4Vectors, jsonlite
vroom, org.At.tair.db, AnnotationDbi, clusterProfiler,
ComplexHeatmap, data.table, DT, edgeR, enrichplot, FactoMineR,
ggpubr, ggrepel, grDevices, grid, httr, limma, magrittr,
methods, mixOmics, MOFA2, plotly, purrr, RColorBrewer,
reshape2, reticulate, rmarkdown, S4Vectors, shiny,
shinydashboard, shinyWidgets, stats, stringr, tidyr, tibble,
tidyselect, UpSetR,
utils, Seqinfo, data.table, IRanges, GenomicRanges, parallel,
Rsamtools
dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors,
tidyr, tools, yaml
Rsamtools, IRanges, S4Vectors, baySeq, Seqinfo, seqLogo
methods, httr2, rjsoncons, dplyr, tidyr, rlang, memoise,
cachem, whisker, jsonlite, GenomicRanges, IRanges, Seqinfo
plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools,
utils, RSQLite
glmnet, pROC, ggplot2, graphics, stats, Biobase, methods,
utils
Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab,
methods, pamr, stats, utils
assertthat, Biobase, ChemmineR, data.table, digest, dplyr,
enviPat, glue, httr, httr2, logger, methods, MSnbase, mzR,
purrr, R.utils, rcdk, readJDX, readr, rjson, S4Vectors, tibble,
tidyselect, webchem, XML, yaml
Rcpp (>= 0.12.8), methods, S4Vectors, GenomicRanges,
SummarizedExperiment, devtools, TBX20BamSubset,
TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, DESeq2,
apeglm, BiocStyle
ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment,
stats, utils, methods
Biobase, BiocGenerics, BiocParallel, stats, limma, dplyr,
magrittr, rlang, edgeR, foreach, mice
affy, boot, impute, splines, graphics, qvalue, reshape2
parallel, grDevices, graphics, utils, stats, methods, grid,
RColorBrewer, gplots, ggplot2, limma, Biobase
Rcpp, stats, Biobase, methods, BiocParallel, lme4
Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods,
patchwork, reshape2, S4Vectors, shiny, shinycssloaders,
shinyFeedback
BiocFileCache, jsonlite, xml2, RCurl, curl, utils
GOSemSim, AnnotationDbi, GO.db, pheatmap, ggplot2, ggrepel,
treemap, tm, wordcloud, shiny, grDevices, grid, stats, methods,
umap
utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25),
IRanges (>= 2.13.12), XVector (>= 0.19.7), bitops,
BiocParallel, stats
methods, stats, igraph, stringr, grDevices, Biobase,
S4Vectors, SummarizedExperiment, BiocGenerics
XML, RCurl, assertthat, stringi, rvest, data.table, xml2,
dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis,
knitr, scales, rmarkdown, htmltools
RedeR, minet, viper, mixtools, snow, stats, limma, data.table,
IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr,
pheatmap, grDevices, graphics, utils
survival, RColorBrewer, grDevices, graphics, stats, utils,
scales, data.table, egg, ggplot2, pheatmap, dunn.test
Biobase, methods, ggplot2, pROC, fdrtool, splines, utils,
tibble
corrplot, MASS, stats, lattice, grDevices, gridExtra,
snowfall, psych, BiocParallel, grid, bladderbatch, reshape2,
graphics
GENLIB, gRain, snpStats, kinship2, methods, stats, utils,
R.utils
httr, utils, XML, rjson, data.table, RCurl, dplyr, tidyr,
readr, stringr, purrr, lubridate
rJava, Biostrings, IRanges, utils, stats, cluster, binom
locfdr, SummarizedExperiment, BiocParallel, limma, pbapply,
ggplot2, boot, Matrix, stats, methods, graphics
Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph,
rmarkdown, knitr, SummarizedExperiment, AnnotationDbi, httr,
KEGGREST, bookdown
Biostrings, pwalign, GenomicRanges, IRanges, data.table,
BiocParallel, methods, Seqinfo, S4Vectors, ggplot2, stats,
stringi, utils, graphics, grid, seqLogo, cowplot
grid, ggplot2, plyr, spatstat.geom, stats, grDevices
reshape2, BiocParallel, ape, scales, Seurat, ggplot2, ggtree,
patchwork, proxy, methods, stats, base, utils, dplyr
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
matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph,
Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils,
methods, survival
grDevices, graphics, stats, utils, dplyr, ggplot2, gtools,
HiCcompare, lattice, mclust, mice, miceadds, ranger, rstatix,
tidyr, rlang, data.table, BiocParallel
dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr,
ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra,
tibble, scales, rlang, flowCore, methods, basilisk,
basilisk.utils, reticulate, here, pwalign, utils
geeM, MASS, mpath, dplyr, stats, utils, withr, purrr, tidyr,
furrr, doSNOW, gamlss, scales, future, Matrix, ggplot2,
splines, foreach, glmmTMB, parallel, RcppEigen, bigstatsr,
tidyselect, broom.mixed, Rcpp
data.table, Rcpp, magrittr, plyr, stringr, utils, stats,
methods, ggplot2, pheatmap, RColorBrewer, rhdf5, readr,
parallel, grDevices
foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats,
phytools, KernelKnn, gplots, zeallot, crayon, assertthat,
igraph, methods, grDevices, graphics, stats, utils, markdown,
SummarizedExperiment, BiocParallel
tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils,
stats, readr
stats, methods, assertthat, tibble, dplyr, purrr, stringr,
Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca,
cluster, kernlab, origami, RSpectra, coop, Matrix,
DelayedArray, ScaledMatrix, MatrixGenerics
stats, utils, methods, graphics, doParallel, foreach,
parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS
(>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>=
4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), BiocParallel (>=
1.12.0)
Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS,
emdbook, magrittr, utils
BiocParallel, Rtsne, grDevices, graphics, stats
S4Vectors, seriation, circlize, methods, randomcoloR, stats,
grid, grDevices, matrixStats
Rsamtools, IRanges, Seqinfo, graphics, grDevices, utils, abind
ggplot2, grid, igraph, utils, yulab.utils
Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix
e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges,
methods, plotly, RColorBrewer, reshape2, rmarkdown, S4Vectors,
stats, utils
graphics, BiocParallel, utils, methods, stringr, readr,
tibble, MASS, wheatmap (>= 0.2.0), GenomicRanges (>= 1.61.1),
IRanges, grid, preprocessCore, S4Vectors, ggplot2,
BiocFileCache, Seqinfo, stats, SummarizedExperiment (>=
1.39.1), dplyr, reshape2
BiocParallel, Matrix, DESeq2, S4Vectors, data.table, edgeR,
openxlsx, pheatmap, stats, circlize, methods, sva
httr, jsonlite, yaml, objectProperties, stringr, S4Vectors,
docopt, curl, uuid, data.table
Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12),
Seqinfo, GenomicRanges (>= 1.31.8), pwalign, hwriter, methods,
lattice, latticeExtra,
beanplot, glmnet, graphics, grDevices, grid, gridBase,
gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC,
RColorBrewer, scales, stats, stringr, utils, infotheo,
progress, corrplot, lmerTest, mlr3learners, mlr3tuning,
paradox, lgr
biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer,
Matrix, SparseM, graphics, stats, utils, SummarizedExperiment,
BiocParallel, methods
stats4, grDevices, graphics, stats, scrime (>= 1.2.5)
AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array,
magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue,
stats, utils, reshape2, visNetwork, BiocParallel, fastmatch,
reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5,
GSEABase, DelayedArray, BiocGenerics, tibble
mzR, ggplot2, grid, reshape2, grDevices, stats, utils
basilisk, BiocParallel, data.table, dplyr, ggplot2, tools,
Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer,
RCurl, reticulate, sparseMatrixStats, SummarizedExperiment,
tidyr
dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges,
Rsamtools, parallel, graphics, stats, utils, methods
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
simona, ComplexHeatmap (>= 2.7.4), grid, circlize, GetoptLong,
digest, tm, GO.db, AnnotationDbi, slam, methods, clue,
grDevices, stats, utils, cluster (>= 1.14.2), colorspace,
GlobalOptions (>= 0.1.0)
Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2,
reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster,
statmod
methods, stats, graphics, ggplot2, grDevices, ggrepel,
GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR,
RColorBrewer, Biobase, BiocParallel, SummarizedExperiment,
matrixStats, reshape2, S4Vectors
S4Vectors, stats, utils, BiocGenerics, GenomeInfoDb, MASS,
IRanges, GenomicRanges
RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree,
graphics, grDevices, gridExtra, methods, parallel, seqinr,
stats, tidytree, utils
magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0)
dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools,
sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils
R6, httr, rlang, purrr, jsonlite, assertthat, data.table,
Matrix, magrittr, methods, stringr, stats, IRanges,
GenomicRanges, SummarizedExperiment
basilisk, reticulate, irlba, stats, assertthat
matrixStats, matrixTests, rstatix, spatstat.explore,
spatstat.geom, ape, hdf5r, nanoparquet, jsonlite, Matrix,
qvalue, stats, utils, methods, ggplot2, reshape2, RColorBrewer,
circlize, mixtools, dplyr, readbitmap, rlang, effsize, viridis
babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet,
checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>=
1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>=
2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix,
methods, plotly (>= 4.9.0), stats, utils, viridis
utils, stats, matrixStats, IRanges, XVector
Rcpp, Matrix, matrixStats (>= 0.60.0), methods
methods, glmnet, huge, stats, graphics, utils
grDevices, stats, utils, graphics, SeuratObject, Biobase,
GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4)
S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML,
scattermore, dplyr, pbapply, data.table, readxl, magick,
grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats,
utils, methods, ggtext, tools, RBioFormats
ProtGenerics (>= 1.39.2), methods, IRanges, MsCoreUtils (>=
1.7.5), graphics, grDevices, stats, tools, utils, fs,
BiocGenerics, MetaboCoreUtils
dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel,
magrittr, HiCcompare, GenomicRanges, utils
Spectra (>= 1.5.6), MsCoreUtils, methods
Spectra (>= 1.19.9), IRanges, S4Vectors, MsCoreUtils,
ProtGenerics, methods
Biobase (>= 2.5.5), graphics, grDevices, gtools, methods,
RColorBrewer, stats, utils
Biobase, stats, ppcor, logging, foreach, doRNG, data.table,
MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse,
caret, dplyr, biomaRt, randomForest, ggridges, cvms,
ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr,
stringr, tidyr
xcms, MSnbase, MsExperiment, RaMS, dplyr, tidyr, tibble,
ggplot2, shiny, plotly, data.table, caret, stats, graphics,
utils, keys
ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork,
gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices,
stats, utils, graphics, doFuture, doRNG, future, foreach
dplyr (>= 1.1), magrittr, rlang, stats, graphite, tibble,
ggraph, igraph, reshape2, org.Hs.eg.db, SummarizedExperiment,
edgeR, methods, ggforce, pheatmap, utils, stringr, gtools,
tidyr
igraph, slam, BiocNeighbors, Matrix, MASS, abind,
SummarizedExperiment, methods, MatrixGenerics, BiocGenerics,
BiocSingular, BiocParallel
Biobase, gridExtra, ggplot2, methods, stats, grid, MASS,
calibrate, gplots, edgeR, limma, foreach, affy
BiocGenerics, dplyr, Seqinfo, GenomicAlignments,
GenomicRanges, gridExtra, IRanges, grid, methods, reshape2,
rlang, stats, stringr, TxDb.Hsapiens.UCSC.hg38.knownGene,
tidyselect
png, sqldf, plyr, igraph, httr, methods, RColorBrewer, gplots,
hash, plotrix
methods, BiocGenerics, XVector, stringr, stringi, crayon,
grDevices
Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra,
networkD3, ggrepel, graphics, stats, org.Hs.eg.db,
AnnotationDbi
data.table, dplyr, tidyr, ggplot2, magrittr, qvalue (>= 1.99),
digest, Biobase
stats, utils, graphics, ggplot2, BiocParallel
utils, stats, tools, Matrix, BiocGenerics (>= 0.51.3),
S4Vectors (>= 0.33.7), IRanges (>= 2.23.9), Seqinfo, S4Arrays
(>= 1.1.1), DelayedArray (>= 0.31.12)
dplyr, nloptr, magrittr, methods, tibble, tidyselect,
BEDASSLE, scales, visNetwork, randomcoloR
assertthat, caret, dplyr, tidyr, rsample, methods, rlang,
utils, Biostrings, stats, SummarizedExperiment
ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta, stats, graphics
matrixStats, stats, graphics, utils, limma, edgeR
data.table, reshape2, ggplot2, stats, grDevices, graphics,
utils, biomaRt, methods
methods, Biostrings, S4Vectors, IRanges, utils, stats,
parallel, graphics, grDevices, RSQLite, DBI
data.table, ggplot2, grDevices, magrittr, methods, patchwork,
RankProd, RColorBrewer, stats, utils
seqinr, methods, Biostrings, stringr, BiocGenerics
Rcpp (>= 1.0.8), BiocParallel, GenomicRanges, rlang,
Biostrings, utils, methods, igraph, stats, grDevices,
RColorBrewer, pheatmap, ggplot2, ggnetwork, intergraph
GenomicRanges, SummarizedExperiment, ggplot2, yaml, stringr,
magrittr, S4Vectors, crayon, BiocGenerics, htmlwidgets
DT, assertthat, bsplus, crayon, dplyr, ggplot2, htmltools,
glue, magrittr, methods, plotly, rlang, rstudioapi, shinyAce,
shinyFiles, shinyWidgets, shinydashboard, shinydashboardPlus
(>= 2.0.0), shinyjqui, shinyjs, shinytoastr, stringr, stats,
styler, tibble, utils, vroom (>= 1.3.1), yaml, R6, RSQLite,
openssl
DESeq2, GGally, Rtsne, SummarizedExperiment, ape, dplyr,
ggplot2, ggrepel, ggtree, glmpca, pheatmap, plotly, tibble,
magrittr, DT, stats
dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2,
tidyr, ggpubr, RColorBrewer, reshape2, cowplot
ape (>= 5.0), phangorn (>= 2.12), rlang, utils, methods, dplyr
BiocGenerics, GenomicRanges, IRanges, matrixStats, methods,
stats, graphics, shiny
ggplot2, ggpubr, methods, miniUI, mzID, mzR, shiny, stats
graphics, grDevices, methods, ncdf4, stats, utils, assertthat
downloader (>= 0.4), grDevices, biomaRt, dplyr, graphics,
tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite
(>= 1.0.0), plyr, knitr, methods, ggplot2, stringr (>= 1.0.0),
IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils,
SummarizedExperiment (>= 1.4.0), TCGAbiolinksGUI.data (>=
1.15.1), readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1)
edgeR, BiocGenerics, reshape2, GenomicRanges, IRanges,
SummarizedExperiment, GenomicAlignments, Rsamtools, e1071,
cluster, ggplot2, grid, grDevices, stats, utils, methods,
locfit
GenomicRanges, rTensor, readr, methods, MOFAdata, tximport,
tximportData, graphics, stats, utils, shiny
TDbasedUFE, Biobase, GenomicRanges, utils, rTensor, methods,
graphics, RTCGA, stats, enrichplot, DOSE, STRINGdb, enrichR,
hash, shiny
S4Vectors, Seqinfo, GenomicRanges, Biobase (>= 2.15.1)
DESeq2, KEGGREST, stats, utils, dplyr, plotly, htmlwidgets,
biomaRt, methods
utils, igraph, methods, graphics, stats, BiocParallel
arules, fields, GenomicRanges, graphics, stringr, methods,
stats, gplots
tibble, dplyr (>= 1.1.0), magrittr, tidyr, stringr, rlang,
purrr, tidyselect, stats, parallel, utils, lifecycle, scales,
ggplot2, SummarizedExperiment, GenomicRanges, methods,
S4Vectors, crayon, Matrix
Biobase, dplyr, flowCore, ggplot2, methods, purrr, rlang,
stats, stringr, tibble, tidyr
dplyr, tibble (>= 3.0.4), magrittr, tidyr, ggplot2, rlang,
purrr, lifecycle, methods, utils, S4Vectors, tidyselect,
ellipsis, vctrs, pillar, stringr, cli, fansi, stats, pkgconfig,
plyxp
methods, AnnotationDbi, gplots, graphics, grDevices, stats,
utils, annotate, DBI, RSQLite
strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4
Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods,
stats
dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr,
ggrepel, lmtest, plyr, checkmate
gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel,
flexclust, grDevices, graphics, Biobase, SPEM
circlize, ComplexHeatmap, data.table, grDevices, grid,
GSEABase, Matrix, methods, stats, utils
methods, stats, utils, grDevices, htmlwidgets, jsonlite,
data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr
stats, methods, SummarizedExperiment, corpcor, doParallel,
parallel, ggplot2, tidyr, GGally
methods, stats, grDevices, reshape2, Rtsne, umap,
RColorBrewer, ggplot2, ggrepel, SummarizedExperiment
grDevices, graphics, animation, tibble, dplyr, stringr, purrr,
methods, shiny, BiocFileCache, readr, tools, plotly, ggplot2
assertthat, caret, ClassifyR, directPA, doParallel, dplyr,
ggnewscale, ggplot2, ggraph, ggrepel, ggthemes, glmnet, Hmisc,
igraph, latex2exp, limma, magrittr, methods, plotly, pROC,
purrr, reshape2, stats, stringr, survival, tibble, tidygraph,
tidyr, statmod
methods, utils, stats, assertthat, ggplot2, scales, grid,
grDevices
grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2),
MSnbase (>= 2.33.5), PSMatch (>= 1.11.4), ggplot2 (>= 2.2.1),
mzR (>= 2.27.5)
SummarizedExperiment, BiocGenerics, S4Vectors, Biobase,
BiocParallel, ggplot2, tibble, dplyr, caTools, downloader,
magrittr, methods, reshape2, tidyr, data.table, assertthat,
scales, graphics, grDevices, parallel, stats, utils, limma,
jsonlite
biobroom, broom, data.table, doParallel, foreach,
futile.logger, ggplot2, grDevices, gridExtra, grid, knitr,
limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr,
purrr, RColorBrewer, RCurl, reshape2, rmarkdown, splines,
stats, stringr, tibble, utils, VennDiagram, VGAM
ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl,
parallel, MASS, BiocParallel, limma
IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base,
stringr, RColorBrewer, methods
biomaRt, data.table, doSNOW, foreach, ggplot2, graphics,
grDevices, igraph, limma, parallel, progress, RedeR, snow,
stats, tidyr, topGO
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
RCy3, KEGGREST, dplyr, purrr, tibble, pbapply
ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble,
tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6)
stats, utils, graphics, grDevices, segmented, gplots,
parallel, magrittr, BiocParallel, DT, S4Vectors,
SummarizedExperiment, methods, shiny, shinyFiles
graphics, utils, stats, dplyr, ggplot2, patchwork, stringr,
tidyr, roll
grDevices, graphics, methods, stats, survival, utils,
siggenes, LogicReg (>= 1.6.1), data.table
shinyjs, shinyFiles, plyr, data.table, DT, stringr,
stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr,
config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices,
graphics, stats, utils, vegan
stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector,
Biostrings, Modstrings, ggplot2, scales
Biostrings, stringr, httr2, xml2, S4Vectors, methods, IRanges,
utils
bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel,
iterators, RColorBrewer, circlize, igraph, grid, gridExtra,
xtable, gtable, scales, R.matlab, grDevices, graphics, stats,
utils, methods
tm, text2vec, tokenizers, textstem, stopwords, data.table,
purrr, DiagrammeR, stats
Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn,
grDevices, graphics, stats, utils
Biobase, graphics, grDevices, splines, stats
class, ggplot2, hexbin, methods, scales, shiny, stats, utils,
RColorBrewer, S4Vectors
methods, stats, httr, jsonlite, S4Vectors (>= 0.47.6)
AnnotationDbi, BiocFileCache, BiocBaseUtils, BiocGenerics,
httr2, jsonlite, methods, progress, rjsoncons, rlang, utils
methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp,
Biostrings, BiocGenerics, S4Vectors, rlang, grid,
MatrixGenerics
igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr,
methods, cluster, Biobase, fpc, BiocGenerics, monocle,
grDevices, graphics, stats, utils
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
MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0),
iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2,
gtools, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack,
rlang, lme4 (>= 1.1.33), grDevices, graphics, Biobase, methods,
utils, stats
Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics,
stats
dplyr, DT, methods, ggplot2, grDevices, magrittr, patchwork,
plotly, purrr, rlang, shiny, stats, tibble, tidyr, htmlwidgets,
utils
utils, data.tree, ape, parallel, Rfast, stats
Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr,
RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment,
tidyr, utils
mixtools, stats, parallel, e1071, KernSmooth
data.table, AnnotationDbi, dendextend, dynamicTreeCut,
GOSemSim, GO.db, heatmaply, topGO, AnnotationForge, DT,
DiagrammeR, R.utils, RColorBrewer, UpSetR, biomaRt, fgsea,
ggplot2, htmlwidgets, igraph, methods, plotly, scales,
ComplexHeatmap, circlize
cowplot, magrittr, Seqinfo, GenomeInfoDb, GenomicAlignments,
RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2,
methods, graphics, stats
matrixStats, limma, parallel, shiny, qvalue, grDevices, stats,
MultiAssayExperiment, clusterProfiler, DOSE, httr, graphics
multtest, qvalue, stats, utils, BiocManager
methods, utils, stats, grDevices, assertthat, S4Vectors,
DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics,
limma, topconfects, dplyr, purrr, ggplot2, rlang, scales,
reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl
utils, methods, cli, Biobase, SummarizedExperiment, config,
golem, shiny, DT, ggplot2, dplyr, rlang, stringr,
shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer,
logging
limma, matrixStats, locfit, stats, graphics
limma, randomForest, kernelshap, caret, lime, DT, methods,
SummarizedExperiment, ggplot2
MSnbase (>= 2.33.3), mzR (>= 2.25.3), methods, Biobase,
BiocGenerics, ProtGenerics (>= 1.37.1), lattice,
MassSpecWavelet (>= 1.66.0), S4Vectors, IRanges,
SummarizedExperiment, MsCoreUtils (>= 1.19.2), MsFeatures,
MsExperiment (>= 1.5.4), Spectra (>= 1.16.1), progress,
RColorBrewer, MetaboCoreUtils (>= 1.11.2), data.table
BiocGenerics, genefilter, graphics, grDevices, gtools,
methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta,
siggenes
methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2,
scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid,
nlme, PharmacoGx, downloader
mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools,
grDevices, graphics, utils, STRINGdb
methods, utils, stats, tools, BiocGenerics, S4Vectors, IRanges
IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table,
grDevices, limma
checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
phyloseq, pscl, ggplot2, MatrixGenerics, SummarizedExperiment,
stats, VGAM, matrixStats, tidyr, tibble, dplyr, DESeq2,
reshape2, RColorBrewer, magrittr, BiocGenerics, graphics, utils
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
S4Vectors, IRanges, XVector, Biostrings, Rhtslib
MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats, hgu95av2.db
knitr, RUnit, BiocGenerics, TENxPBMCData, CHETAH, stringr,
LoomExperiment
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, BiocStyle, knitr, rmarkdown, purrr, ggpattern,
ggplot2, cowplot, tidyverse, magick
knitr, BiocStyle, testthat (>= 3.0.0), BiocManager
BiocManager, BiocGenerics, S4Vectors, Seqinfo, GenomeInfoDb,
GenomicRanges, AnnotationHub, ExperimentHub, ensembldb, httr,
tidyr, r3dmol, bio3d, shiny, shiny.gosling, ggdist, colorspace,
knitr, rmarkdown, testthat (>= 3.0.0)
ASICS, BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5),
GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr,
NMRphasing, plotly (>= 4.7.1), progressr, SummarizedExperiment,
S4Vectors, testthat (>= 2.0.0), writexl (>= 1.0), zip (>=
2.0.4)
plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db,
hgu133acdf, Rgraphviz, RColorBrewer
mia (>= 1.6.0), DT, S4Vectors, SingleCellExperiment,
SummarizedExperiment, TreeSummarizedExperiment, dplyr, knitr,
magrittr, microbiome, phyloseq, rmarkdown, testthat, tidyr,
tidyverse
ExperimentHub, SNFtool, knitr, rmarkdown, testthat
BiocStyle, biomformat, devtools, glmnet, knitr, rmarkdown,
testthat, usethis
BiocFileCache, BiocStyle, knitr, processx, rhdf5 (>= 2.52.1),
rmarkdown, S4Vectors, Seurat, SeuratObject,
SingleCellExperiment, spelling, SummarizedExperiment, testthat
(>= 3.0.0), vctrs, withr, yaml
hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges,
rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db,
org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, BiocStyle, knitr
utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db,
RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,
reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75,
BiocStyle, knitr
BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown
biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy,
hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db,
rmarkdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit
IRanges, Seqinfo, GenomeInfoDb, GenomicRanges,
VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr,
AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR,
Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment,
ExperimentHub, gdsfmt, rmarkdown, HubPub
knitr, rmarkdown, testthat, withr, readr, BiocStyle,
devtools, AnVILAz, AnVILGCP, lifecycle
BiocStyle, dplyr, knitr, readr, rmarkdown, tinytest
AnVIL, AnVILAz, AnVILGCP, BiocStyle, knitr, rmarkdown,
testthat (>= 3.0.0), tinytest
AnVIL, BiocStyle, knitr, rmarkdown, testthat, withr
knitr, BiocStyle, GCPtools, testthat (>= 3.0.0)
DESeq2, airway, knitr, rmarkdown, testthat
BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR,
knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat
AssessORFData, BiocStyle, knitr, rmarkdown, RSQLite (>= 1.1)
testthat, BiocStyle, lintr, knitr, rmarkdown
Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery,
knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne,
testthat, zoo
affy, AnnotationDbi, AnnotationHub, apcluster, Biobase,
BiocManager, BiocStyle, Biostrings, coin, diagram, DBI, e1071,
ensembldb, GenomicDataCommons, GenomicRanges, GEOquery,
ggstance, ggridges, ggtext, hgu95av2.db, ICSNP, jsonlite,
knitr, lmerTest, MASS, mclust, mixOmics, mixtools, mpm, nlme,
OlinkAnalyze, org.Hs.eg.db, org.Mm.eg.db, patchwork,
pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite,
remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer,
statmod, testthat, UniProt.ws, writexl, XML
AWAggregatorData, BiocStyle, ExperimentHub, knitr, rmarkdown,
testthat (>= 3.0.0)
airway, ggplot2, testthat, EDASeq, knitr, BiocStyle,
RefManageR, sessioninfo, rmarkdown
RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, testthat, roxygen2
testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, testthat, tximport, BiocStyle,
GenomicFeatures, Biostrings
testthat, interp, fields, pheatmap, viridis, rmarkdown,
spelling
knitr, rmarkdown, methods, testthat, BiocStyle
knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle
knitr, rmarkdown, BiocStyle, testthat, callr
testthat, BiocStyle, knitr, rmarkdown, rcmdcheck,
BiocParallel, HDF5Array, beachmat.hdf5
testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix
testthat, BiocStyle, knitr, rmarkdown, Matrix
testthat, BiocStyle, knitr, rmarkdown, pander, seewave
testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr,
rmarkdown, dplyr, ggplot2, spelling
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle
rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle
BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>=
3.0.0)
BiocStyle, RCurl, biomaRt, knitr, knitcitations,
knitrBootstrap, testthat, ggplot2, rmarkdown
tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr,
limma
limma, DESeq2, airway, ggplot2, plyr, GenomicRanges,
testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase,
rmarkdown, SummarizedExperiment
BiocFileCache, BiocStyle, GenomicFeatures, GenomeInfoDbData,
knitr, httr2, rmarkdown, rvest, tinytest, txdbmaker,
TxDb.Hsapiens.UCSC.hg19.knownGene
BiocStyle, knitr, testthat (>= 3.0.0), rmarkdown
knitr, testthat, rjsoncons, igraph, BiocStyle
testthat, knitr, BiocStyle, rmarkdown, rtracklayer
Biobase, S4Vectors, IRanges, S4Arrays, SparseArray,
DelayedArray, HDF5Array, GenomicRanges, pwalign, Rsamtools,
AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase,
annotate, MultiAssayExperiment, RUnit
BiocManager, BiocStyle, curl, glue, knitr, rmarkdown,
sessioninfo, shinytest2
BiocParallel, testthat, BiocStyle, knitr, rmarkdown
airway, BiocStyle, boot, DESeq2, ggplot2 (>= 3.4.1),
GOSemSim, Hmisc, knitr (>= 1.43), org.Hs.eg.db, reactome.db,
rmarkdown, spelling, testthat (>= 3.1.5), WGCNA
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
BiocStyle, here, knitr, rmarkdown, testthat (>= 3.0.0)
GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache,
GO.db, testthat, knitr, rmarkdown, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix
testthat, HDF5Array, BiocStyle, rmarkdown, knitr
BiocStyle, covr, devtools, knitr, pkgdown, RefManageR,
rmarkdown, sessioninfo, testthat, utils
BiocGenerics, BiocPkgTools, knitr, commonmark, BiocStyle
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, xml2
BiocStyle, httptest2, knitr, mockery, rmarkdown, testthat (>=
3.0.0)
knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2,
networkD3, covr
rgl, impute, DLBCL, genefilter, xtable, ALL, limma,
hgu95av2.db, XML
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
testthat, knitr, rmarkdown, BiocStyle, arm, earth, ranger,
SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1)
testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl
RUnit, devtools, BiocGenerics, knitr, rmarkdown
knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut,
scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans,
kohonen, apcluster, DirichletMultinomial, vegan, fastcluster
BiocStyle, knitr, rmarkdown, RUnit,
BSgenome.Hsapiens.UCSC.hg19
knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit
lifecycle, tidyverse, shiny (>= 1.9.1), bslib (>= 0.8.0),
BiocStyle, knitr, rmarkdown, testthat
testthat, BiocStyle, knitr, rmarkdown, devtools
testthat (>= 3.0.0), IRanges, knitr, rmarkdown, BiocStyle,
rtracklayer
BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>=
3.0.0)
BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat
(>= 3.1.6)
BiocStyle, knitr, msqc1, RefManageR, rmarkdown, sessioninfo,
testthat, vdiffr
BiocStyle, testthat, knitr, rmarkdown, emmeans, lme4,
lmerTest
RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0),
sessioninfo
EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6),
hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma,
lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db
knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db,
limma, affy, genefilter, rmarkdown
knitr, arules, concaveman, ReactomePA, bnviewer, rmarkdown,
withr, BiocStyle, testthat (>= 3.0.0)
knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
knitr, BiocStyle, BiocGenerics, testthat, RUnit
BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown
BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation
BiocStyle, caret, knitr, testthat, rmarkdown
CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle,
ExperimentHub
knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics,
BiocManager, kableExtra, rgl
data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics,
zellkonverter, SingleCellExperiment, HDF5Array, tidyr,
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery
BiocStyle, knitr, rmarkdown, testthat, ggplot2
airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager,
rmarkdown,RUnit,codetools
RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL,
BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs,
png,rmarkdown, BiocManager,bibtex,codetools
argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat,
GenomeInfoDb, Rsamtools, GenomicInteractions, GenomicRanges,
IRanges, AnnotationHub
BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix,
BiocStyle, testthat, rmarkdown, knitr
BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene,
BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr
mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit,
BiocGenerics
msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19),
testthat, knitr (>= 1.1.0), rmarkdown, mzR (>= 2.41.4),
MsBackendMetaboLights (>= 1.3.1), vdiffr, RColorBrewer
Rsamtools, GenomicAlignments, RNAseqData.HNRNPC.bam.chr14,
BSgenome.Hsapiens.UCSC.hg19, testthat, knitr, rmarkdown,
BiocStyle
BiocStyle, knitr, rmarkdown, testthat, webshot
limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot,
BiocStyle, pamr, PoiClaClu, knitr, htmltools, gtable, scales,
e1071, rmarkdown, IRanges, robustbase, glmnet, class,
randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale,
TOP, BiocNeighbors
testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown,
BRAIN, UniProt.ws (>= 2.36.5)
BiocParallel, knitr, rmarkdown, testthat, CAMERA
knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr,
CluMSIDdata, metaMS, metaMSdata, xcms
RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2
yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt
AnnotationHub, knitr, jsonlite, readr, rmarkdown,
org.Hs.eg.db, prettydoc, BiocManager, testthat
knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics,
covr
BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork
MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics,
gbm, mgcv, corpcor, limma, st, mvtnorm
minet, Rgraphviz, RUnit, BiocGenerics, igraph
testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle,
rmarkdown, covr
genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen,
NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE,
AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree,
dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot,
flexclust, randomForest, e1071
flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny,
testthat, devtools, flowWorkspaceData, ggplot2, progress
BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq,
TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree,
tidytree, statmod, covr, sva, tcltk
testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff,
fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport,
grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12),
gridGraphics, gplots, rmarkdown, Cairo, magick
knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19),
MsBackendMgf
knitr, BiocStyle, rmarkdown, testthat, Seurat
BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra,
magick, Cairo, limma
pander, markdown, BiocStyle, rmarkdown, knitr, formatR,
testthat
Biobase, knitr, rmarkdown, testthat, BiocStyle
testthat, knitr, rmarkdown, piano, ggplot2
BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl,
rtracklayer, sangerseqR, testthat, VariantAnnotation
hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit
AnnotationDbi, org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures,
GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager
rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr,
igraph, dplyr
testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown,
SummarizedExperiment, SingleCellExperiment
testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes
BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown,
testthat
magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr
knitr, rmarkdown, MatrixGenerics, htmltools, RUnit,
BiocGenerics, BiocManager, BiocStyle, Biobase
testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown,
BiocStyle, HDCytoData
testthat, flowWorkspaceData , knitr, rmarkdown, parallel
testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown,
BiocStyle, reshape2, dplyr, CytoPipelineGUI
testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown,
BiocStyle, patchwork
testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph,
diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR,
factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster,
forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr,
norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr,
limma, preprocessCore, stringr, tidyr, impute, gplots,
grDevices, reshape2, graphics, stats, methods, ggplot2,
RColorBrewer, Matrix, org.Sc.sgd.db
EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa,
SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle,
edgeR
testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse,
rmarkdown, BiocStyle
Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA,
knitr, limma, readxl, rmarkdown, S4Vectors,
SummarizedExperiment, testthat, covr
glmnet (>= 4.1-7), GSVA, viper, fgsea (>= 1.15.4), AUCell,
SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr,
pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo,
pheatmap, testthat, OmnipathR, Seurat, ggplot2, ggrepel,
patchwork, magick
BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat
corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL,
rrcov, Rgraphviz, NCIgraph
BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown,
statmod, testthat
BiocParallel, HDF5Array (>= 1.17.12), genefilter,
SummarizedExperiment, airway, lobstr, DelayedMatrixStats,
knitr, rmarkdown, BiocStyle, RUnit
testthat, knitr, rmarkdown, BiocStyle, SeqArray, GDSArray
testthat, knitr, rmarkdown, BiocStyle, microbenchmark,
profmem, HDF5Array, matrixStats (>= 1.0.0)
testthat, knitr, BiocStyle, rmarkdown, Matrix
markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr,
dplyr, reticulate
BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown,
testthat (>= 3.0.0)
knitr, rmarkdown, BiocStyle, ggplot2, uwot, testthat
uwot, testthat, knitr, rmarkdown, BiocStyle
testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble,
ggplot2, missForest, pheatmap, RColorBrewer, ggrepel,
BiocStyle, ggbeeswarm
sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19),
RefManageR, rmarkdown (>= 0.3.3), testthat, covr
testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer,
apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply,
airway, glmGamPoi, BiocManager
knitr, tidyverse, rmarkdown, testthat, BiocStyle, IHW
GenomeInfoDb, GenomicFeatures, txdbmaker, pasilla (>=
0.2.22), BiocStyle, knitr, rmarkdown, testthat,
pasillaBamSubset, GenomicAlignments, roxygen2, glmGamPoi
BiocStyle, GenomeInfoDb, GenomicRanges, IRanges, knitr,
rmarkdown, sessioninfo, testthat (>= 3.0.0), tibble
BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST
testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata,
BiocStyle, reshape2, utils
lattice, parallel, MASS, RColorBrewer, DT, knitr, rmarkdown,
BiocStyle
msigdbr, org.Hs.eg.db, org.Mm.eg.db, minfi, knitr, rmarkdown,
GO.db, KEGGREST, testthat,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
IlluminaHumanMethylation450kanno.ilmn12.hg19, BiocStyle, RUnit
knitr, rmarkdown, BiocGenerics, RUnit, tinytest, BiocStyle,
Biostrings
AnnotationHub, knitr, rmarkdown, testthat,
BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19,
caret
BiocStyle, ggplot2, Hmisc, kableExtra, knitr, pheatmap,
rmarkdown, testthat (>= 3.0.0), withr, airway
knitr, patchwork, rmarkdown, Seurat, testthat, formatR,
BiocFileCache, SingleCellExperiment
BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat
prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, memoise,
org.Hs.eg.db, rmarkdown, testthat
PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid,
BiocStyle, knitr, testthat
BiocStyle, knitr, rmarkdown, tidyverse, testthat (>= 3.0.0)
limma, convert, GEOquery, dyebiasexamples, methods
knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment,
viper
knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager,
devtools, BiocStyle
distill, BiocStyle, knitr, readxl, edgeR, limma, EDASeq,
statmod
BiocStyle (>= 2.32.1), BSgenome (>= 1.72.0),
BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr,
rmarkdown, RUnit (>= 0.4.33)
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)
knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie,
Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38,
ensembldb, AnnotationDbi, GenomicFeatures, txdbmaker,
rtracklayer, withr
SummarizedExperiment, testthat, Biobase, survminer,
affycoretools, knitr, plotROC, limma, rmarkdown
testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter,
RColorBrewer
clusterProfiler, dplyr, europepmc, ggarchery, ggupset, glue,
knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr,
ggforce, ggHoriPlot, AnnotationDbi, ggplotify, ggridges,
grDevices, gridExtra, ggstar, scales, ggtreeExtra, tidydr
BiocStyle, knitr, rmarkdown, ggplot2, scatterpie, ggtangle,
ggrepel, testthat, ggnetwork, magick
GenomeInfoDb, SummarizedExperiment, VariantAnnotation, RUnit,
knitr, rmarkdown, ggplot2
roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase,
testthat
knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown,
GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle
knitr, rmarkdown, testthat (>= 3.0.0), sessioninfo
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown,
EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick
BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat
(>= 3.0.0)
ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL,
hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db
knitr, BiocStyle, rmarkdown, HubPub, GenomicAlignments
testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle
BiocStyle, countrycode, knitr, rmarkdown, testthat (>= 3.0.0)
BiocFileCache, BiocStyle, ggtree, graphics, knitr, memuse,
rmarkdown, spelling, testthat (>= 3.0.0)
rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0)
biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr
shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown,
testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi,
GOSemSim
BiocStyle, testthat, knitr, rmarkdown, topGO
knitr, rmarkdown, GOstats, GO.db, BiocGenerics, pROC, RUnit,
BiocStyle
RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics,
org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, BiocManager
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
RUnit, BiocGenerics, knitr, markdown, rmarkdown
knitr, rmarkdown, stringr, tidyverse, testthat
BiocStyle, dplyr, knitr, rmarkdown, testthat (>= 2.1.0)
BiocStyle, testthat, CytoML, flowWorkspace, ggrepel,
scattermore, pheatmap, ggpointdensity
testthat, knitr, rmarkdown, BiocStyle, DepecheR
xtable, testthat, openCyto, ggcyto, ggridges
knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, stats,
flowClust, openCyto, flowStats, ggcyto
colorspace, flowStats, knitr, rmarkdown, markdown, testthat
testthat, flowWorkspaceData (>= 2.23.2), knitr, rmarkdown,
ggcyto, parallel, CytoML, openCyto
BiocStyle, knitr, knitcitations, knitrBootstrap,rmarkdown,
codetools
BiocStyle, covr, ggrepel, kableExtra, knitr,
metabolomicsWorkbenchR, POMA, rmarkdown, rvest,
SummarizedExperiment, testthat (>= 2.3.2), tidyverse
oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM,
hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf,
hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData
knitr, rmarkdown, testthat (>= 3.0.0), MultiAssayExperiment,
SummarizedExperiment, airway
pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase,
Rsamtools, GenomicAlignments,
TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma
testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi,
org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils
knitr, ggplot2, testthat, BEDMatrix, genio
edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db,
BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea
affydata, tools, splines, hgu95av2cdf, hgu95av2probe
BiocStyle, BumpyMatrix, futile.logger, gDRstyle (>= 1.7.1),
gDRtestData (>= 1.7.1), kableExtra, knitr, markdown, purrr,
rmarkdown, SummarizedExperiment, testthat, yaml
BiocStyle, gDRstyle (>= 1.7.1), gDRimport (>= 1.7.1),
gDRtestData (>= 1.7.1), IRanges, knitr, pkgbuild, qs, testthat,
yaml
BiocStyle, gDRtestData (>= 1.7.1), gDRstyle (>= 1.7.1),
knitr, purrr, qs, testthat
BiocManager, BiocStyle, futile.logger, gDRstyle (>= 1.7.1),
gDRtestData (>= 1.7.1), IRanges, knitr, lintr, mockery, purrr,
rcmdcheck, rmarkdown, scales, testthat, tools, withr, yaml
parallel, digest, Matrix, crayon, RUnit, knitr, markdown,
rmarkdown, BiocGenerics
knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown
testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2,
ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap,
viridis, poolr, listviewer, shiny
apcluster, GEOquery, knitr, rmarkdown, BiocStyle
class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer,
BiocStyle, knitr
GeneMeta, breastCancerVDX, breastCancerMAINZ,
breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT,
breastCancerNKI, rmeta, Biobase, xtable, knitr, caret,
survival, BiocStyle, magick, rmarkdown
RUnit, BiocGenerics, RBGL, knitr, shiny, STRINGdb, BiocStyle,
magick, rmarkdown, org.Hs.eg.db
RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown,
Fletcher2013b, geneplast.data, geneplast.data.string.v91,
ggplot2, ggpubr, plyr
Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db,
BiocStyle, knitr
knitr, rmarkdown, foreach, doRNG, doParallel, Biobase,
SummarizedExperiment, testthat, methods, BiocStyle
spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr
GenomeInfoDbData, R.utils, data.table, GenomicRanges,
Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2,
BSgenome.Hsapiens.NCBI.GRCh38, RUnit, 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
AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle,
rmarkdown, GenomicDistributionsData
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
RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation,
gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader,
data.table, DT, magrittr, shinydashboard,
BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38,
MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v4.0.GRCh38,
SNPlocs.Hsapiens.dbSNP144.GRCh37,
TxDb.Hsapiens.UCSC.hg38.knownGene
knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis,
BiocStyle, testthat, forcats, stats, wordcloud, circlize,
EnrichmentBrowser, clusterProfiler, msigdbr, cluster,
RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr,
utils
testthat, knitr, BiocStyle, rmarkdown, covr,
GenomicAlignments, Biostrings, GenomeInfoDb
VAExprs, stringdist, knitr, testthat, rmarkdown
BiocCheck, roxygen2, knitr, rmarkdown, testthat
knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud
rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph,
Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork
knitr, rmarkdown, BiocGenerics, testthat, covr, markdown,
quarto, DropletUtils, SingleCellExperiment
knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr,
clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi,
IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq,
testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery,
BiocGenerics
devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat
(>= 3.0.0)
airway, knitr, DESeq2, recount3, rmarkdown, stringr, testthat
(>= 3.0.0)
airway, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat,
vdiffr
testthat, flowWorkspaceData, knitr, rmarkdown, flowStats,
openCyto, flowViz, ggridges, vdiffr
knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle,
AnnotationDbi, testthat (>= 3.0.0)
ggtreeExtra, ape, cowplot, knitr, rmarkdown, readxl,
ggnewscale, kableExtra, gggenes, statebins, prettydoc, testthat
(>= 3.0.0), yulab.utils
Biostrings, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr,
prettydoc, rmarkdown, testthat, tibble, glue, Biostrings
aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust,
rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils
treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc,
markdown, testthat (>= 3.0.0), pillar
knitr, prettydoc, rmarkdown, BiocStyle, testthat (>= 3.0.0)
roxygen2, knitr, rmarkdown, testthat, BiocStyle
GO.db, golubEsets, hu6800.db, vsn, Rgraphviz
vsn, golubEsets, KEGGREST, hu6800.db, Rgraphviz, GO.db,
lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS,
boot, rpart, mstate
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
BiocManager, BiocStyle, knitr, rmarkdown, org.At.tair.db,
org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db,
org.Dm.eg.db, org.Dr.eg.db, org.EcSakai.eg.db, org.EcK12.eg.db,
org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Rn.eg.db,
org.Sc.sgd.db, org.Ss.eg.db, org.Pt.eg.db, org.Xl.eg.db, GO.db,
ggplot2, ggrepel, DT, magick
hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter,
RColorBrewer, xtable, SparseM, GSEABase, geneplotter,
org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr
knitr, rmarkdown, RUnit, BiocManager, BiocGenerics,
BiocStyle, devtools
SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle,
knitr
checkmate, a4Preproc, ALL, BiocStyle, clipper, codetools,
hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db,
parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat,
topologyGSA (>= 1.4.0)
hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools,
testthat, BiocStyle, knitr, RUnit
GSEABase,Category, multtest, ALL, annotate, hgu95av2.db,
genefilter, GOstats, RColorBrewer
knitr, rmarkdown, BiocStyle, clusterProfiler, testthat, tm
knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp,
Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP,
iC10TrainingData, pamr, testthat
testthat (>= 1.0.0), knitr, RColorBrewer, markdown,
rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff
BiocStyle, knitr, rmarkdown, formatR, rrBLUP
ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings,
GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors,
VariantAnnotation, parallel, BiocStyle, knitr
knitr, rmarkdown, testthat, BiocStyle, digest, jsonvalidate,
DBI, RSQLite, S4Vectors, methods
BiocParallel, ExperimentHub, TENxBrainData, HDF5Array,
testthat, knitr, rmarkdown, BiocStyle
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, SingleCellExperiment, DelayedMatrixStats,
genefilter, RSpectra, RUnit, knitr, rmarkdown, BiocStyle
RColorBrewer, pheatmap, MASS, patchwork, testthat
BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown,
statmod, testthat (>= 3.2.2), vdiffr (>= 1.0.8)
BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray,
knitr, markdown, rmarkdown, Rsamtools
knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5
HiContacts, HiContactsData, BiocFileCache, rtracklayer,
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
HiContactsData, rtracklayer, GenomicFeatures, Biostrings,
BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra,
patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
rhdf5, BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0)
knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0),
markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown
knitr, annotate, gwascat, testthat, rmarkdown
org.Hs.eg.db, GO.db, AnnotationDbi, knitr, BiocStyle,
testthat, rmarkdown, dplyr, DT
EDASeq, testthat, knitr, rmarkdown, BiocStyle
testthat (>= 3.0.0), knitr, ggplot2, rmarkdown, BiocStyle,
pryr
AnnotationHubData, ExperimentHubData, GenomeInfoDbData,
testthat, knitr, rmarkdown, BiocStyle,
SingleCellExperiment, SummarizedExperiment, Seurat,
SeuratObject, ggplot2, progress, testthat, splatter, scater,
devtools, knitr, rmarkdown, BiocStyle, ExperimentHub
BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0)
knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot,
DescTools, RColorBrewer
knitr, rmarkdown, pwalign, msa, ape, testthat, seqinr
knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
GenomicAlignments, parallel, testthat, knitr, rmarkdown,
BiocStyle, ggplot2, dplyr, scales, ggseqlogo
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2,
ggforce, ggrepel, patchwork
BiocStyle, GenomicAlignments, knitr, Rsamtools, rtracklayer,
RUnit, shinytest2, VariantAnnotation
ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat,
Matrix, BiocStyle, knitr, rmarkdown, devtools
RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2),
BiocStyle
BiocManager, BiocStyle, knitr, curl, glue, rmarkdown,
sessioninfo, testthat, tibble, GenomicDataCommons
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), DT
BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT
testthat (>= 3.0.0), ggfortify, shinyWidgets, pROC, tuneR,
knitr, curl, readxl, reshape2, vroom, here, enrichR, rmarkdown
knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071
knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0),
SummarizedExperiment
knitr, rmarkdown, testthat, EnrichedHeatmap, GenomicRanges,
data.table, circlize, GenomicFeatures, tidyverse, tidyHeatmap,
cluster, org.Hs.eg.db, simplifyEnrichment, GO.db, SC3,
GOexpress, SingleCellExperiment, scater, gplots, pheatmap,
airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve
(>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks
testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite,
processx, attempt, BiocStyle, httr
gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, gridExtra, testthat,
minionSummaryData
RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr
XVector, GenomicRanges, Rsamtools, GenomicAlignments,
GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset,
RUnit, BiocStyle
testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown,
roxygen2, withr, extraDistr, ggalluvial, scales, gridExtra,
R.utils, RefManageR, flexdashboard, circlize, plotly, gtools,
eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr,
future, doFuture, foreach, psych, Rcapture
BiocFileCache, BiocStyle, bsseq, ggplot2, ggridges, knitr,
microbenchmark, rmarkdown, GenomicRanges, IRanges, Rsamtools,
SummarizedExperiment, S4Vectors, testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, htmltools, RUnit, dplyr
MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots,
RColorBrewer, gridExtra, limma, boot, DBI, MASS
IsoCorrectoRGUI, knitr, rmarkdown, testthat, BiocStyle
knitr, png, limma, grid, DT, randomForest, digest, testthat,
rmarkdown, BiocStyle, magick, statmod, codetools
RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db,
SPIA
RUnit, BiocGenerics, BiocStyle, knitr, markdown
testthat (>= 3.0.0), SummarizedExperiment, rmarkdown, knitr,
sesame, gprofiler2, ggrastr
BiocManager, BiocStyle (>= 2.26), httptest, knitr, lattice,
msdata, OrgMassSpecR, protViz, S4Vectors, Spectra, testthat,
mzR
BiocGenerics, BiocStyle, testthat, knitr, rmarkdown
RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats,
VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75,
Rsamtools, GenomicFiles (>= 1.13.6)
BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines,
affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio,
org.Hs.eg.db, vsn
BiocStyle, pander, rmarkdown, car, gridExtra, knitr, testthat
(>= 3.0.0)
BiocStyle, ggplot2, magick, testthat (>= 3.0.0), knitr,
rmarkdown, caret, ROTS
MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer,
moments, testthat, matrixStats
knitr, rmarkdown, igraph, reshape2, limma,
BiocStyle, devtools, knitr, roxygen2, rmarkdown, testthat (>=
3.0.0), S4Vectors,
LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2,
testthat
testthat, knitr, rmarkdown, BiocStyle, MACSdata
berryFunctions, Biostrings, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr,
mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment,
rmarkdown, S4Vectors
BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo,
testthat (>= 3.0.0)
devtools, markdown, renv, testthat, BiocManager, knitr,
rmarkdown, roxygen2, mockery, covr, magick, BiocStyle
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
Matrix, sparseMatrixStats, SparseArray, DelayedArray,
DelayedMatrixStats, SummarizedExperiment, testthat (>= 2.1.0)
knitr, markdown, BiocStyle, testthat (>= 3.0.0)
gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr,
pander, devtools, testthat, GSVA
testthat, knitr, rmarkdown, fgsea, BiocManager
covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer,
derfinder, GenomeInfoDb, tools, RefManageR, testthat
cowplot, BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0),
knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1),
rmarkdown, covr
shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>=
1.4.0), org.Hs.eg.db, clusterProfiler,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>=
2.22.0), BiocStyle
BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra,
knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0)
testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny,
shinyjs, msentropy, DT, microbenchmark, mzR
BiocStyle, testthat, knitr, rmarkdown, robustbase
BiocStyle, knitr, rmarkdown, DT, ggraph, tidyverse, testthat
(>= 3.0.0)
BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr
(>= 1.48), testthat (>= 3.2.1.1)
BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0)
BiocStyle, doParallel, testthat, knitr, rmarkdown
BiocStyle, knitr, rmarkdown, devtools, R.utils
BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat
rmarkdown, knitr, testthat (>= 3.0.0), prettydoc
rmarkdown, prettydoc, testthat, knitr, nlme, phangorn,
DECIPHER, randomForest, jsonlite, biomformat, scales, yaml,
withr, S4Vectors, purrr, seqmagick, glue, ggupset,
ggVennDiagram, ggalluvial (>= 0.11.1), forcats, phyloseq,
aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext,
DirichletMultinomial, ggpp, BiocManager
testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle
knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind,
affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1
human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18,
BSgenome.Hsapiens.UCSC.hg19, RUnit
BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny
BiocStyle, knitr, rmarkdown, R.cache, SPONGE
BiocStyle, covr, earth, future, igraph (>= 1.2.7), iml,
kernlab, knitr, MASS, rmarkdown, RSNNS, testthat (>= 3.0.0),
xgboost
stringi, testthat (>= 2.1.0), HGNChelper,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Biobase, BiocStyle, GSVA, methods, rmarkdown, knitr,
SummarizedExperiment, testthat
BiocStyle, knitr, rmarkdown, mime, testthat, microbenchmark,
magick, vdiffr, kableExtra, devtools
class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL,
hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07),
golubEsets, ada, keggorthology, kernlab, mboost, party, klaR,
BiocStyle, knitr, testthat, airway
GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Cf.eg.db, org.Mmu.eg.db, KEGGREST, annotate, Rgraphviz,
GOstats, graph, limma, mouse4302.db, reactome.db
knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM,
BiocStyle
testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown,
markdown, covr, BiocStyle
testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny,
shinyFiles, shinydashboard, shinyjs
BiocStyle, knitr, rmarkdown, testthat, usethis
knitr, testthat, Seurat, SeuratObject, ggpubr, foreach,
psych, MultiAssayExperiment, SummarizedExperiment,
SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown,
data.table, tidyverse, BiocStyle, Matrix, markdown
BiocStyle, knitr, rmarkdown, testthat, viper
destiny, Hmisc, knitr, Seurat, scater, testthat
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2,
png, edgeR
knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat
(>= 3.0.0)
knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc
AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
extraChIPs (>= 1.13.3), ggdendro, knitr, MASS, MotifDb,
rmarkdown, rtracklayer, SimpleUpset, testthat (>= 3.0.0), VGAM
Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign
rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
RSQLite, rmarkdown
testthat, rmarkdown, mzR, knitr, BiocStyle
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
rmarkdown
BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr,
lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5),
testthat
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
RSQLite, msdata, rmarkdown, microbenchmark, mzR
testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD,
impute, norm, pcaMethods, vsn, Matrix, preprocessCore,
missForest
ExperimentHubData, DT, BiocStyle, knitr, rmarkdown, testthat
(>= 3.0.0), Spectra, mzR, PSMatch, QFeatures (>= 1.13.3)
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
rmarkdown, rpx, mzR, msdata, MsBackendSql (>= 1.3.2), RSQLite
testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown
BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2,
tinytest
testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>=
1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.43.3), magick,
msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub,
BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots,
XML, shiny, magrittr, SummarizedExperiment, Spectra
knitr, testthat (>= 3.0.0), downloadthis, DT, rmarkdown,
BiocStyle, imputeLCMD
MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown,
msPurityData, CAMERA, RPostgres, RMySQL
multcomp, gridExtra, knitr, BiocStyle, RefManageR,
sessioninfo, rmarkdown, testthat, tidyverse, plotly, MsDataHub,
MSnbase, matrixStats, MsCoreUtils, covr
BiocStyle, knitr, rmarkdown, tinytest, covr, markdown,
mockery, kableExtra
data.table, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0),
mockery, MSstatsConvert
BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight
BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr
knitr, rmarkdown, tinytest, covr, mockery, testthat (>=
3.0.0)
MSstats, MSstatsTMT, tidyverse, boot, purrr, gridExtra,
knitr, rmarkdown, BiocStyle, testthat
rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 3.0.0),
shinytest2,
BiocStyle, HDF5Array, h5mread, knitr, maftools,
RaggedExperiment, reshape2, rmarkdown, survival, survminer,
testthat, UpSetR
knitr, rmarkdown, gplots, RUnit, BiocGenerics,
preprocessCore, Biobase, GEOquery
org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db,
org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db,
org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, knitr, rmarkdown,
BiocStyle, testthat (>= 2.1.0)
BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2)
testthat, BiocStyle, knitr, covr, rmarkdown
testthat (>= 3.0.0), BiocStyle, knitr, Biostrings, pwalign,
plotly, scattermore, BiocManager
RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19),
knitr, XML, rmarkdown
biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf
grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly,
rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx
knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics
knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle
AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db,
rmarkdown, testthat (>= 3.0.0), tidyverse
rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown,
BiocStyle
RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db,
org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db,
org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr,
markdown
BiocStyle, Cairo, DT, knitr, pander, readr, testthat,
truncnorm
BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth,
knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>=
4.0.0), spatstat.explore, stringr, survival, tidyverse,
testthat (>= 3.0.0)
knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics
(>= 0.8.0)
knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle
BiocStyle, fpc, igraph, knitr, missForest, notameViz,
notameStats, pcaMethods, RUVSeq, testthat
batchCorr, BiocStyle, igraph, knitr, notameStats, pcaMethods,
Rtsne, testthat
testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2,
BiocStyle
ALL, genefilter, limma, hgu95av2.db, ReportingTools,
BiocStyle
BiocStyle, BiocGenerics, knitr, rmarkdown, testthat
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
hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6,
pd.genomewidesnp.5, pd.mapping50k.hind240,
pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp,
genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6),
RUnit, human370v1cCrlmm, VanillaICE, crlmm
BiocStyle, knitr, rmarkdown, testthat, GEOquery,
VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges,
FDb.InfiniumMethylation.hg19, snpStats
knitr, rmarkdown, BiocStyle, magick, testthat
RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis,
desc, testthat (>= 3.0.0)
testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle
BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown,
bookdown, pander
flowWorkspaceData, knitr, rmarkdown, markdown, testthat,
utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2),
MASS
airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2,
gridExtra, knitr, Matrix, rmarkdown, scales, testthat
rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown,
testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape,
phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB
BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat
(>= 3.0.0)
knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra,
grid, reshape2, scales
biomartr, knitr, rmarkdown, testthat, dendextend, biocViews,
BiocCheck, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA,
ggplot2, ggrepel, car, cowplot, reshape2
writexl, readxl, readr, rhdf5, plotly, testthat (>= 3.0.0),
knitr, rmarkdown, BiocStyle, covr
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges,
gwascat, BiocStyle, rmarkdown
AnnotationDbi, BiocStyle, biomaRt, covr, DESeq2, jsonlite,
knitr, org.Hs.eg.db, rmarkdown, scales, testthat (>= 3.0.0),
vdiffr
airway, circlize, grDevices, knitr, RCurl, reshape2,
rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse
BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb
testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr,
HDF5Array
testthat (>= 3.0.0), tidyverse, rmarkdown, styler, cli,
lintr, rtracklayer, knitr, devtools, ggplot2, BiocStyle,
BiocManager, usethis, utils, AnnotationHub, GenomeInfoDb
testthat, devtools, faahKO, msdata, knitr, rmarkdown, pander,
BiocStyle
diffviewer, gridExtra, testthat (>= 3.0.0), vdiffr,
rmarkdown, BiocStyle, knitr, withr, qpdf, shinytest2, devtools,
R.devices, usethis, rlang, magick, cowplot
statmod, BiocStyle, knitr, rmarkdown, tidyr
knitr, markdown, rmarkdown, BiocStyle, PepsNMRData
testthat, BiocStyle, knitr, rmarkdown, org.Hs.eg.db,
org.Mm.eg.db
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5,
GEOquery
pander, rmarkdown, knitr, knitcitations, crayon, testthat,
markdown, BiocStyle, R.utils
knitr, rmarkdown, forcats, testthat, BiocStyle,
SingleCellExperiment
testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq,
SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr,
mia
BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr,
withr
testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown,
org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle,
stringr, calibrate
yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM,
gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown,
BiocStyle
GenomeInfoDb, knitr, rtracklayer, testthat, BiocStyle,
prettydoc, BSgenome, BSgenome.Dmelanogaster.UCSC.dm6,
BiocManager, rmarkdown, ggplot2
ExperimentHub, mixOmics, ggplot2, testthat, tidyr, scales,
minfi, EpiDISH, knitr, rmarkdown
BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>=
3.0.0)
knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf,
BiocStyle, biocViews, testthat (>= 3.0.0)
knitr, htmltools, BiocStyle, rmarkdown, testthat
devtools, knitr, rmarkdown, testthat, airway, IRanges, here
testthat (>= 3.0.0), knitr, rmarkdown, ddPCRclust
BiocStyle, covr, ggraph, ggtext, knitr, patchwork, plotly,
tidyverse, testthat (>= 2.3.2)
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics
BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2,
BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi
quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata
airway, biomaRt, BiocFileCache, broom, Seurat,
SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl,
pheatmap, tibble, rmarkdown, testthat (>= 2.1.0)
testthat, rmarkdown, pRolocdata (>= 1.43.2), roxygen2,
xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr,
akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13),
nipals, reshape, magick, umap
pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown, testthat
(>= 3.0.0)
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, DT
msdata, rpx, mzID, mzR, SummarizedExperiment, BiocStyle,
rmarkdown, knitr, factoextra, vdiffr (>= 1.0.0), testthat
knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData,
ropls
pumadata, affydata, snow, limma, ROCR,annotate
MotifDb, BSgenome, BSgenome.Dmelanogaster.UCSC.dm3,
PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel,
PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background,
BiocStyle, knitr
affy, MSnbase, ggplot2, lattice, mzR, BiocStyle, rmarkdown,
markdown
SingleCellExperiment, MsDataHub (>= 1.3.3), Matrix,
HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny,
shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn,
preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute,
norm, ComplexHeatmap
Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute,
imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr,
rmarkdown
devtools, DESeq2, knitr, rmarkdown, testthat, BiocStyle
bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat
BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR,
rmarkdown, sessioninfo, testthat (>= 3.0.0)
testthat, BiocStyle, knitr, rmarkdown, covr
AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery,
knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat,
tibble
QUBICdata, qgraph, fields, knitr, rmarkdown
rmarkdown, BiocStyle, knitr, pander, markdown
BiocStyle, knitr, rmarkdown, testthat, GenomeInfoDb,
MultiAssayExperiment
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
knitr, rmarkdown, pander, BiocStyle,
BSgenome.Ecoli.NCBI.20080805
knitr, BiocParallel, lme4, nlme, rmarkdown, BiocStyle,
testthat (>= 2.1.0), limma, sva
markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>=
3.0.0)
BiocStyle, covr, knitr, rmarkdown, testthat (>= 3.0.0), withr
BiocStyle (>= 2.28), ExperimentHub, tartare, knitr, testthat
BiocStyle (>= 2.5), ExperimentHub, knitr, protViz (>= 0.7),
rmarkdown, tartare (>= 1.5), testthat
Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr
Rgraphviz, RCurl, graph, RUnit, BiocGenerics, RBGL, igraph
testthat, parallel, BiocStyle, knitr, rmarkdown
knitr, RColorBrewer, sqldf, BiocGenerics, testthat,
BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW,
parallel, rmarkdown
knitr, BiocStyle, knitcitations, sessioninfo, rmarkdown,
testthat, covr
BiocStyle, testthat, knitr, rmarkdown, base64enc, graph
BiocStyle, knitr, rmarkdown, igraph, grDevices
BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db,
prettydoc, testthat
testthat, igraph, XML, BiocManager, RCurl, bookdown,
rappdirs, yaml, BiocParallel, OSCA.intro, OSCA.workflows
knitr, rmarkdown, markdown, BiocStyle, TreeAndLeaf
knitr, rmarkdown, testthat, biocViews, BiocCheck, BiocStyle,
airway
GEOquery, rmarkdown, knitr, BiocManager, testthat
testthat, BiocStyle, knitr, rmarkdown, BiocSingular
BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2,
corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl
mclust, flexmix, testthat, BiocStyle, knitr, formatR,
rmarkdown
R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics,
RUnit
testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra,
BiocManager, stringr, stringi, ggplot2, tibble, lipidr
RUnit, BiocStyle, BiocGenerics, xtable, sna
bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr,
ggplot2, mockery, BiocParallel, curl
knitr, testthat, BiocStyle, DT, rmarkdown
BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.47.7)
BiocStyle, knitr, rmarkdown, tinytest, mockery
knitr, rmarkdown, BiocManager, BiocStyle, testthat (>= 3.0.0)
knitr, rmarkdown, testthat (>= 3.0.0), plyranges,
plotgardener, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene
BiocStyle, knitr, rmarkdown, testthat, devtools
BiocStyle, CAMERA, gplots, knitr, magick, rmarkdown,
RMassBankData (>= 1.33.1), RUnit, xcms (>= 1.37.1)
readxl, knitr, rmarkdown, reshape2, pander, testthat
BiocStyle, knitr, PCAtools, rmarkdown, tidyr, stringr,
testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, GSEABenchmarkeR,
EnrichmentBrowser, preprocessCore, DESeq2
knitr, rmarkdown, testthat, RUnit, BiocGenerics
BiocStyle, covr, kableExtra, knitr, rmarkdown, styler,
testthat (>= 3.0.0)
Biostrings, BiocStyle, testthat, knitr, tibble, rmarkdown
knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0),
shinydashboard, DT, plotly, heatmaply, magrittr, utils,
clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db,
org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db,
org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db,
org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db,
org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db
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
testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret,
e1071, parallel, doParallel
BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer, pwalign
Rtsne, ape, Seurat, knitr, rmarkdown, tictoc, BiocStyle,
testthat (>= 3.0.0)
devtools, testthat, pander, Biobase, GenomicRanges, IRanges,
S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations,
RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation,
RTCGA.CNV, magrittr, tidyr
RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
knitr, BiocStyle, TPP, testthat, rmarkdown
RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt,
Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db,
org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, GEOquery, affy, airway, QUBIC
knitr, rmarkdown, DESeq2, limma, SummarizedExperiment,
airway, BiocStyle, matrixTests, BiocManager
knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation
BiocParallel, SparseArray (>= 0.0.4), DelayedArray,
HDF5Array, testthat, knitr, rmarkdown, BiocStyle
IRanges, GenomicRanges, SummarizedExperiment, Matrix,
DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle,
knitr
GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP,
survival, foreach, doRNG, Rgraphviz, GOstats
BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db,
markdown, rmarkdown, RUnit
knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub,
ensembldb, edgeR, DEXSeq, stageR, DelayedArray
testthat, BiocStyle, knitr, rmarkdown, BiocSingular,
DelayedMatrixStats
BiocStyle, knitr, testthat, cluster, SingleCellExperiment
knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db,
rmarkdown
testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment,
SummarizedExperiment, scRNAseq, cowplot
knitr, rmarkdown, testthat, BiocStyle, DT, gridExtra
BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0)
covr, grid, coop, uwot, scran, ggh4x, knitr, UCell, irlba,
rlang, magick, igraph, scater, gtable, ggpubr, viridis,
bluster, cluster, circlize, speedglm, rmarkdown, gridExtra,
BiocStyle, slingshot, gprofiler2, GenomeInfoDb, BiocParallel,
BiocGenerics, BiocNeighbors, ComplexHeatmap, Seurat (>= 5.0.0),
testthat (>= 3.0.0), SingleCellExperiment, SummarizedExperiment
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM,
R.utils
knitr, rmarkdown, roxygen2, shiny, testthat (>= 3.0.0)
BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat
(>= 3.0.0), yaml
DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0),
covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter,
SingleCellExperiment, microbenchmark
BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown,
testthat
emojifont, knitr, rmarkdown, prettydoc, tibble
testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown
GenomeInfoDb, GenomicRanges, BSgenome, GenomicFeatures,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Celegans.UCSC.ce2, RUnit,
knitr, rmarkdown, BiocStyle
BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics,
BiocStyle
scales, BiocManager, GenomeInfoDb, knitr, DNAcopy, e1071,
randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle,
ggrepel, grDevices, KernSmooth, pals
testthat, parallel, knitr, rmarkdown, BiocStyle
BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi,
knitr
BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr
testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx
knitr, testthat, rmarkdown, BiocStyle, signatureSearchData,
DT
curl, knitr, matrixStats, rmarkdown, Seurat (>= 5.0.0),
SeuratObject (>= 5.0.0), testthat (>= 3.0.0)
RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments,
rtracklayer, 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
knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan,
igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics,
flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11),
shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter,
gridtext, fpc
BiocStyle, knitr, biomaRt, stringr, monocle
pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr
BiocStyle, devtools, knitr, magick, rmarkdown, testthat
BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater,
splatter, testthat (>= 3.0.0), tidytext, UpSetR
BiocManager, bit64, covr, knitcitations, knitr (>= 1.6),
devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat
(>= 2.1.0)
knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0)
parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS,
BiocGenerics
data.table, devtools, knitr, cowplot, rjson, rmarkdown,
BiocStyle, testthat (>= 3.0.0), CoGAPS, ComplexHeatmap
AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle,
DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin,
KernSmooth, knitr, magrittr, matrixStats, msigdbr (>= 10.0),
orthogene, PANTHER.db (>= 1.0.3), R.utils, reactome.db,
rmarkdown, SummarizedExperiment, statmod, stringr, testthat,
webshot
HDF5Array, ExperimentHub, testthat, knitr, rmarkdown,
BiocStyle
testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle
testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>=
5.0.0)
testthat, knitr, rmarkdown, qpdf, Seurat
knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), stringi,
qpdf, pheatmap, viridis, cowplot, vdiffr, sf
BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown,
RUnit (>= 0.4)
testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2,
BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0),
rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick
BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown,
microbenchmark, testthat, covr
testthat, msdata (>= 0.19.3), roxygen2, rmarkdown, knitr,
S4Vectors, BiocStyle, mzR
testthat, quarto, MsBackendMgf, MsDataHub, mzR, knitr,
BiocStyle
testthat, knitr, rmarkdown, ggplot2, tidyr
BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI, dplyr,
ggplot2
testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra,
digest, doParallel, bigmemory, GSVA
BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3),
RUnit
BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools,
knitr, pander, patchwork, rmarkdown, spelling, testthat (>=
3.0.0), tidyverse
scran, scater, knitr, UpSetR, gridExtra,
SingleCellMultiModal, BiocStyle, magrittr, testthat (>= 3.0.0),
purrr, sparseMatrixStats
knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma,
DEXSeq, testthat
RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>=
1.3), roxygen2, doSNOW
BiocStyle, knitr, magrittr, rmarkdown, testthat
testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle
limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr
devtools, MutationalPatterns, RUnit, BiocManager,
BiocGenerics, BiocStyle, knitr, rmarkdown
GenomeInfoDb (>= 1.45.5), rhdf5, HDF5Array (>= 1.7.5),
annotate, AnnotationDbi, GenomicFeatures, SparseArray,
SingleCellExperiment, TxDb.Hsapiens.UCSC.hg19.knownGene,
hgu95av2.db, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown,
RUnit, testthat, digest
rmarkdown, markdown, knitr, testthat (>= 3.0.0)
flowCore, knitr, rmarkdown, usethis, testthat (>= 3.0.0),
BiocSingular, bluster, scater, scran, Seurat,
SingleCellExperiment, BiocStyle, magick, qs2
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
knitr, rmarkdown, ggplot2, testthat, VariantAnnotation
knitr, testthat (>= 3.0.0), gplots, htmltools, BiocParallel
Hmisc, clinfun, xtable, Biobase, BiocManager
pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat
BiocStyle, knitr, rmarkdown, testthat (>= 3.1.6)
dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2,
rmarkdown, testthat
knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse,
BiocStyle
BiocStyle, knitr, igraph, markdown, rmarkdown
BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc,
glue
rtracklayer, BiocStyle, ggtree, labdsv, covr, knitr,
rmarkdown, testthat (>= 3.0.0), xml2, networkD3
BiocStyle, knitr, rmarkdown, systemPipeRdata,
GenomicAlignments, grid, dplyr, testthat, rjson, annotate,
AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT,
rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools,
GenomicFeatures, txdbmaker, GenomeInfoDbData, VariantAnnotation
(>= 1.25.11)
testthat, BiocStyle, knitr, rmarkdown, systemPipeR (>=
2.12.0), systemPipeRdata (>= 2.10.0), rhandsontable, zip,
callr, pushbar, fs, readr, R.utils, DESeq2,
SummarizedExperiment, glmpca, pheatmap, grid, ape, Rtsne,
UpSetR, tidyr, esquisse (>= 1.1.0), cicerone
systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>=
3.0.0), BiocGenerics, Biostrings, methods
BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr,
pheatmap, SpectralTAD, magick, qpdf
tinytest, BiocStyle, ggimage, knitr, rmarkdown
testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS,
covr
BiocStyle, knitr, msdata, sessioninfo, rmarkdown, gridExtra,
testthat (>= 3.0.0), covr
BiocStyle, bugsigdbr, fgsea, knitr, rmarkdown, testthat
jpeg, png, BiocStyle, rmarkdown, devtools, maftools,
parmigene, c3net, minet, Biobase, affy, testthat, sesame,
AnnotationHub, ExperimentHub, pathview, clusterProfiler,
Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph,
limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra,
survival, doParallel, parallel, ggrepel (>= 0.6.3), scales,
grid, DT
knitr, rmarkdown, testthat (>= 3.0.0), RTCGA.rnaseq,
RTCGA.clinical, BiocStyle, MOFAdata
apeglm, BiocStyle, knitr, rmarkdown, testthat
BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager,
Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva,
GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, widyr,
clusterProfiler, msigdbr, DESeq2, broom, survival, boot,
betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional,
survminer, tidySummarizedExperiment, markdown, uwot,
matrixStats, preprocessCore, igraph, EGSEA, IRanges, here,
glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS, pkgconfig,
enrichplot, patchwork, airway
BiocStyle, HDCytoData, knitr, RefManageR, rmarkdown,
sessioninfo, testthat (>= 3.0.0)
rmarkdown, knitr, BiocStyle, biomaRt, RCy3, testthat (>=
3.0.0)
BiocStyle, testthat, knitr, markdown, rmarkdown, plotly,
rbibutils, prettydoc, airway
drosgenome1.db, puma, lumi, BiocStyle, BiocManager
knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat
BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse,
igraph, gplots
knitr, aroma.light, affxparser, RUnit, BiocGenerics
GenomicFeatures, shiny, BiocManager, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix
knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData,
ggbeeswarm, ggsci, survminer, tidyverse
limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat,
reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr,
rmarkdown, BiocStyle
topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat,
BiocStyle, xml2
ALL, hgu95av2.db, hgu133a.db, genefilter, multtest,
Rgraphviz, globaltest, knitr, BiocStyle, rmarkdown
rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools,
PharmacoGx, xtable, markdown
testthat, roxygen2, knitr, BiocStyle, rmarkdown
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr,
geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer
Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown,
phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml
BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap,
sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0),
tibble, tidyr, SingleCellExperiment
BiocStyle, knitr, rmarkdown, kableExtra, testthat (>= 3.0.0)
haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1),
KernSmooth, VariantAnnotation
rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer
BiocGenerics, shinycssloaders, tidyverse, BiocManager,
Biostrings, xtable, rlist, motifStack, knitr, rmarkdown,
testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr
knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport
BiocGenerics, knitr, rmarkdown, testthat, httptest,
BiocStyle, rtracklayer
BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways,
magick
fgsea, knitr, testthat, reticulate, rmarkdown
devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle
knitr, rmarkdown, testthat, tximportData,
TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow,
limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats,
Matrix, eds
DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown,
BiocStyle
spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb,
testthat, BiocParallel, seqLogo, motifStack, dplyr, ape,
ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio
GenomicRanges, SummarizedExperiment, InteractionSet,
SingleCellExperiment, MultiAssayExperiment, BiSeq, testthat,
knitr, rmarkdown, BiocStyle
BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend,
tximport, tximportData, ballgown, DESeq2, RUnit, cowplot,
Rfast, zenith, statmod, BiocGenerics, r2glmm, readr
knitr, markdown, RColorBrewer, rmarkdown, rstudioapi,
testthat (>= 3.0.0)
htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr,
rmarkdown, corrplot, remotes, BiocManager, stats, utils,
grDevices, processx
GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,
testthat, covr, knitr, rmarkdown, pkgdown
knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, httr
affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr,
testthat
knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR,
EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi,
ComplexHeatmap, patchwork, testthat (>= 2.1.0)
MSnbase, testthat, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR
knitr, ggforce, shapr (>= 1.0.1), airway, xgboost,
BiocGenerics, RUnit, S4Vectors
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, rhdf5
BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat
knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), tidyverse,
microbiome
doMC, doMPI, doSNOW, doParallel, doRedis
parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Hs.eg.db, org.Dm.eg.db
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