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MatrixGenerics SummarizedExperiment HDF5Array methods utils Rcpp JASPAR2014: methods Biostrings curatedOvarianData: affy BiocGenerics subSeq: data.table dplyr tidyr ggplot2 magrittr qvalue digest Biobase easierData: ExperimentHub AnnotationHub utils SummarizedExperiment ChIC.data: genomeIntervals randomForest caret NPARC: dplyr tidyr BiocParallel broom MASS rlang magrittr stats methods JASPAR2016: methods BSgenome.Hsapiens.NCBI.GRCh38: BSgenome timeOmics: mixOmics dplyr tidyr tibble purrr magrittr ggplot2 stringr ggrepel propr lmtest plyr RCX: jsonlite plyr igraph methods knn.covertree: Rcpp RcppEigen Matrix methods shadowtext: ggplot2 grid scales JASPAR2018: methods Ckmeans.1d.dp: Rcpp Rdpack EpiTxDb: AnnotationDbi Modstrings methods utils httr xml2 curl GenomicFeatures GenomicRanges GenomeInfoDb BiocGenerics BiocFileCache S4Vectors IRanges RSQLite DBI Biostrings tRNAdbImport ggseqlogo: ggplot2 data.table: methods LinTInd: ggplot2 parallel stats S4Vectors data.tree reshape2 networkD3 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stats utils JASPAR2020: methods AgiMicroRna: methods Biobase limma affy preprocessCore affycoretools R.utils: R.oo methods utils tools R.methodsS3 FScanR: stats SplicingFactory: SummarizedExperiment methods stats MADSEQ: rjags VGAM coda BSgenome BSgenome.Hsapiens.UCSC.hg19 S4Vectors methods preprocessCore GenomicAlignments Rsamtools Biostrings GenomicRanges IRanges VariantAnnotation SummarizedExperiment GenomeInfoDb rtracklayer graphics stats grDevices utils zlibbioc vcfR SANTA: igraph graphics Matrix methods stats edgeR: limma methods graphics stats utils locfit Rcpp ggdist: tidyselect dplyr ggplot2 rlang scales grid HDInterval tibble vctrs withr distributional numDeriv glue chemometrics: rpart class e1071 MASS nnet pcaPP robustbase som lars pls mclust OmnipathR: checkmate crayon curl digest dplyr httr igraph jsonlite later logger magrittr progress purrr rappdirs readr readxl rlang rmarkdown stats stringr tibble tidyr tidyselect tools utils withr xml2 yaml evobiR: seqinr ape geiger shiny phytools hypergraph: methods utils graph RAREsim: nloptr rpart: graphics stats grDevices JADE: clue graphics assertive.code: assertive.base assertive.properties assertive.types methods gghighlight: ggplot2 dplyr ggrepel lifecycle purrr rlang tibble MetaboAnnotation: BiocGenerics MsCoreUtils MetaboCoreUtils ProtGenerics methods S4Vectors Spectra BiocParallel SummarizedExperiment QFeatures graphics SpatialCPie: colorspace data.table digest dplyr ggforce ggiraph ggplot2 ggrepel grid igraph lpSolve methods purrr readr rlang shiny shinycssloaders shinyjs shinyWidgets stats SummarizedExperiment tibble tidyr tidyselect tools utils zeallot NISTunits: hgug4112a.db: methods AnnotationDbi org.Hs.eg.db utils: DBI: methods ggcyto: methods ggplot2 flowCore ncdfFlow flowWorkspace plyr scales hexbin data.table RColorBrewer gridExtra rlang pkgbuild: callr cli crayon desc prettyunits R6 rprojroot withr ASICS: BiocParallel ggplot2 glmnet grDevices gridExtra methods mvtnorm PepsNMR plyr quadprog ropls stats SummarizedExperiment utils Matrix zoo paletteer: prismatic rematch2 rlang rstudioapi methylSig: bsseq DelayedArray DelayedMatrixStats DSS IRanges GenomeInfoDb GenomicRanges methods parallel stats S4Vectors widgetTools: methods utils tcltk selectKSigs: HiLDA magrittr gtools methods Rcpp clusterStab: Biobase methods PathNetData: remotes: methods stats tools utils lexicon: data.table syuzhet conicfit: pracma geigen zoo: stats utils graphics grDevices lattice sctransform: dplyr magrittr MASS Matrix methods future.apply future ggplot2 reshape2 rlang gridExtra matrixStats RcppArmadillo Rcpp ABSSeq: methods locfit limma shinyMatrix: shiny jsonlite praise: BUMHMM: devtools stringi gtools stats utils SummarizedExperiment Biostrings IRanges fitdistrplus: MASS grDevices survival methods stats garfield: batchtools: backports base64url brew checkmate data.table digest fs parallel progress R6 rappdirs stats stringi utils withr BOBaFIT: dplyr NbClust ggplot2 ggbio grDevices stats tidyr GenomicRanges ggforce stringr plyranges methods utils magrittr HGNChelper: methods utils limma: grDevices graphics stats utils methods mapproj: maps stats graphics catnet: methods stats utils graphics pepXMLTab: XML SingleCellSignalR: BiocManager circlize limma igraph gplots grDevices edgeR SIMLR data.table pheatmap stats Rtsne graphics stringr foreach multtest scran utils SpacePAC: iPAC oppar: Biobase methods GSEABase GSVA tseries: graphics stats utils quadprog zoo quantmod HTqPCR: Biobase RColorBrewer limma affy gplots graphics grDevices methods stats stats4 utils affycompData: methods Biobase affycomp mlr3misc: backports checkmate data.table digest methods R6 shinyscreenshot: base64enc jsonlite shiny uuid BSgenome.Hsapiens.1000genomes.hs37d5: BSgenome psych: mnormt parallel stats graphics grDevices methods lattice nlme miaSim: SummarizedExperiment TreeSummarizedExperiment deSolve stats poweRlaw gtools S4Vectors MatrixGenerics genArise: locfit tkrplot methods graphics grDevices stats tcltk utils xtable SNPRelate: gdsfmt methods ExperimentHub: methods BiocGenerics AnnotationHub BiocFileCache utils S4Vectors BiocManager curl rappdirs superheat: dplyr ggplot2 gtable magrittr plyr scales ggdendro httpcache: digest httr utils vcfR: ape dplyr graphics grDevices magrittr memuse methods pinfsc50 Rcpp stats stringr tibble utils vegan viridisLite condiments: slingshot mgcv RANN stats SingleCellExperiment SummarizedExperiment utils magrittr dplyr Ecume methods pbapply matrixStats BiocParallel TrajectoryUtils igraph distinct rbenchmark: CluMSIDdata: DeMixT: parallel Rcpp SummarizedExperiment knitr KernSmooth matrixcalc rmarkdown matrixStats stats truncdist base64enc ggplot2 DeMAND: KernSmooth methods RGraph2js: utils whisker rjson digest graph PSEA: Biobase MASS aCGH: cluster survival multtest Biobase grDevices graphics methods stats splines utils BiocOncoTK: methods utils ComplexHeatmap S4Vectors bigrquery shiny stats httr rjson dplyr magrittr grid DT GenomicRanges IRanges ggplot2 SummarizedExperiment DBI GenomicFeatures curatedTCGAData scales ggpubr plyr car graph Rgraphviz yulab.utils: utils SPOTlight: ggplot2 NMF Matrix matrixStats nnls SingleCellExperiment stats pingr: processx utils rsemmed: igraph methods magrittr stringr dplyr survivalsvm: survival pracma quadprog kernlab Matrix stats Hmisc pqsfinder: Biostrings Rcpp GenomicRanges IRanges S4Vectors methods BH HarmanData: MetaVolcanoR: methods data.table dplyr tidyr plotly ggplot2 cowplot parallel metafor metap rlang topconfects grDevices graphics stats htmlwidgets qvalue: splines ggplot2 grid reshape2 gridGraphics: grid graphics grDevices SNPhoodData: gaga: Biobase coda EBarrays mgcv simplifyEnrichment: BiocGenerics grid GOSemSim ComplexHeatmap circlize GetoptLong digest tm GO.db org.Hs.eg.db AnnotationDbi slam methods clue grDevices graphics stats utils proxyC Matrix cluster colorspace GlobalOptions DEP: ggplot2 dplyr purrr readr tibble tidyr SummarizedExperiment MSnbase limma vsn fdrtool ggrepel ComplexHeatmap RColorBrewer circlize shiny shinydashboard DT rmarkdown assertthat gridExtra grid stats imputeLCMD cluster STexampleData: ExperimentHub SpatialExperiment utils CancerInSilico: Rcpp methods utils graphics stats BH TNBC.CMS: e1071 quadprog SummarizedExperiment GSVA pheatmap grDevices RColorBrewer pracma GGally R.utils forestplot ggplot2 ggpubr survival grid stats methods gage: graph KEGGREST AnnotationDbi GO.db mdqc: cluster MASS ReportingTools: methods knitr utils Biobase hwriter Category GOstats limma lattice AnnotationDbi edgeR annotate PFAM.db GSEABase BiocGenerics grid XML R.utils DESeq2 ggplot2 ggbio IRanges smurf: catdata glmnet graphics MASS Matrix methods mgcv parallel RColorBrewer Rcpp speedglm stats RcppArmadillo fBasics: timeDate timeSeries stats grDevices graphics methods utils MASS spatial gss stabledist prismatic: graphics farver grDevices EnsDb.Hsapiens.v75: ensembldb Risa: Biobase methods Rcpp biocViews affy xcms bnlearn: methods EnsDb.Hsapiens.v79: ensembldb oneSENSE: webshot shiny shinyFiles scatterplot3d Rtsne plotly gplots grDevices graphics stats utils methods flowCore loo: checkmate matrixStats parallel stats hgu133aprobe: AnnotationDbi DFP: methods Biobase ResidualMatrix: methods Matrix S4Vectors DelayedArray SBMLR: XML deSolve PECA: ROTS limma affy genefilter preprocessCore aroma.affymetrix aroma.core branchpointer: caret plyr kernlab gbm stringr cowplot ggplot2 biomaRt Biostrings parallel utils stats BSgenome.Hsapiens.UCSC.hg38 rtracklayer GenomicRanges GenomeInfoDb IRanges S4Vectors data.table BAGS: breastCancerVDX Biobase AmpAffyExample: affy BUScorrect: gplots methods grDevices stats SummarizedExperiment pd.hugene.1.0.st.v1: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors chipenrich: AnnotationDbi BiocGenerics chipenrich.data GenomeInfoDb GenomicRanges grDevices grid IRanges lattice latticeExtra MASS methods mgcv org.Dm.eg.db org.Dr.eg.db org.Hs.eg.db org.Mm.eg.db org.Rn.eg.db parallel plyr rms rtracklayer S4Vectors stats stringr utils rScudo: methods stats igraph stringr grDevices Biobase S4Vectors SummarizedExperiment BiocGenerics googleCloudStorageR: assertthat cli curl googleAuthR httr jsonlite openssl utils yaml zip rWikiPathways: httr utils XML rjson data.table tidyr RCurl cummeRbund: BiocGenerics RSQLite ggplot2 reshape2 fastcluster rtracklayer Gviz methods plyr S4Vectors Biobase beadarrayExampleData: Biobase methods beadarray EnsDb.Hsapiens.v86: ensembldb pageRank: GenomicRanges igraph motifmatchr stats utils grDevices graphics IRISFGM: Rcpp MCL anocva Polychrome RColorBrewer colorspace AnnotationDbi ggplot2 org.Hs.eg.db org.Mm.eg.db pheatmap AdaptGauss DEsingle DrImpute Matrix Seurat SingleCellExperiment clusterProfiler ggpubr ggraph igraph mixtools scater scran stats methods grDevices graphics utils knitr gatingMLData: casper: Biobase IRanges methods GenomicRanges BiocGenerics coda EBarrays gaga gtools GenomeInfoDb GenomicFeatures limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM MsCoreUtils: methods S4Vectors MASS stats clue Rcpp Seurat: methods cluster cowplot fitdistrplus future future.apply ggplot2 ggrepel ggridges graphics grDevices grid httr ica igraph irlba jsonlite KernSmooth leiden lmtest MASS Matrix matrixStats miniUI patchwork pbapply plotly png RANN RColorBrewer Rcpp RcppAnnoy reticulate rlang ROCR Rtsne scales scattermore sctransform SeuratObject shiny spatstat.core spatstat.geom stats tibble tools utils uwot RcppEigen RcppProgress HubPub: available usethis biocthis dplyr aws.s3 fs BiocManager utils ggbio: methods BiocGenerics ggplot2 grid grDevices graphics stats utils gridExtra scales reshape2 gtable Hmisc biovizBase Biobase S4Vectors IRanges GenomeInfoDb GenomicRanges SummarizedExperiment Biostrings Rsamtools GenomicAlignments BSgenome VariantAnnotation rtracklayer GenomicFeatures OrganismDbi GGally ensembldb AnnotationDbi AnnotationFilter rlang gaia: CytoDx: doParallel dplyr glmnet rpart rpart.plot stats flowCore grDevices graphics utils GSE62944: Biobase GEOquery snowfall: snow h5vcData: flowGraph: effsize furrr future purrr ggiraph ggrepel ggplot2 igraph Matrix matrixStats stats utils visNetwork htmlwidgets grDevices methods stringr stringi Rdpack data.table gridExtra prettyunits: BEclear: BiocParallel futile.logger Rdpack Matrix data.table Rcpp abind stats graphics utils methods dixonTest ids cvms: checkmate data.table dplyr ggplot2 lifecycle lme4 MuMIn parameters plyr pROC purrr rearrr recipes rlang stats stringr tibble tidyr utils exomeCopy: IRanges GenomicRanges Rsamtools stats4 methods GenomeInfoDb Fletcher2013a: limma Biobase VennDiagram gplots grid imager: magrittr Rcpp methods stringr png jpeg readbitmap grDevices purrr downloader igraph humanStemCell: Biobase hgu133plus2.db breastCancerNKI: Fletcher2013b: Fletcher2013a RTN RedeR igraph RColorBrewer plier: methods affy Biobase ChIPpeakAnno: methods IRanges GenomicRanges S4Vectors AnnotationDbi BiocGenerics Biostrings DBI dplyr 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methods BiocGenerics Biostrings data.table Rcpp utils S4Vectors ShortRead IRanges GenomicRanges GenomeInfoDb BiocParallel gtable gridExtra ggplot2 ggthemes waffle stringr stats matrixStats Matrix dplyr rmarkdown knitr clusterCrit XtraSNPlocs.Hsapiens.dbSNP144.GRCh37: BSgenome methods utils BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges easyRNASeq: Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings edgeR GenomeInfoDb genomeIntervals GenomicAlignments GenomicRanges SummarizedExperiment graphics IRanges LSD locfit methods parallel rappdirs Rsamtools S4Vectors ShortRead utils XtraSNPlocs.Hsapiens.dbSNP144.GRCh38: BSgenome methods utils BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges geneplast: methods igraph snow ape grDevices graphics stats utils data.table biwt: robustbase MASS HDTD: stats Rcpp RcppArmadillo metagene2: R6 GenomicRanges BiocParallel rtracklayer tools GenomicAlignments GenomeInfoDb IRanges ggplot2 Rsamtools purrr data.table methods dplyr magrittr reshape2 dyebias: marray Biobase twoddpcr: class ggplot2 hexbin methods scales shiny stats utils RColorBrewer S4Vectors tibble: fansi lifecycle magrittr methods pillar pkgconfig rlang utils vctrs GUIDEseq: GenomicRanges BiocGenerics BiocParallel Biostrings CRISPRseek ChIPpeakAnno data.table matrixStats BSgenome parallel IRanges S4Vectors GenomicAlignments GenomeInfoDb Rsamtools hash limma dplyr GenomicFeatures crisprBowtie: methods BiocGenerics Biostrings BSgenome crisprBase GenomeInfoDb GenomicRanges IRanges Rbowtie readr stats stringr utils mimager: Biobase BiocGenerics S4Vectors preprocessCore grDevices methods grid gtable scales DBI affy affyPLM oligo oligoClasses MassSpecWavelet: lsa: SnowballC qckitfastq: magrittr ggplot2 dplyr seqTools zlibbioc data.table reshape2 grDevices graphics stats utils Rcpp rlang RSeqAn mouse4302cdf: utils AnnotationDbi scCB2: SingleCellExperiment SummarizedExperiment Matrix methods utils stats edgeR rhdf5 parallel DropletUtils doParallel iterators foreach Seurat pcxnData: beeswarm: stats graphics grDevices utils drosgenome1.db: methods AnnotationDbi org.Dm.eg.db verification: methods fields boot CircStats MASS dtw graphics stats InTAD: methods S4Vectors IRanges GenomicRanges MultiAssayExperiment SummarizedExperiment stats BiocGenerics Biobase rtracklayer parallel graphics mclust qvalue ggplot2 utils ggpubr OncoSimulR: Rcpp parallel data.table graph Rgraphviz gtools igraph methods RColorBrewer grDevices car dplyr smatr ggplot2 ggrepel stringr MethReg: dplyr plyr GenomicRanges SummarizedExperiment DelayedArray ggplot2 ggpubr tibble tidyr S4Vectors sesameData sesame AnnotationHub ExperimentHub stringr readr methods stats Matrix MASS rlang pscl IRanges sfsmisc progress utils callr: processx R6 utils broom.mixed: broom coda dplyr forcats methods nlme purrr stringr tibble tidyr furrr proDA: stats utils methods BiocGenerics SummarizedExperiment S4Vectors extraDistr openxlsx: grDevices methods Rcpp stats stringi utils zip assertive.data: assertive.base assertive.strings mco: minet: infotheo Kendall: boot GenomicTools: gMWT Rcpp data.table GenomicTools.fileHandler circlize stringr snpStats RcppArmadillo BSgenome.Scerevisiae.UCSC.sacCer1: BSgenome MSstatsPTM: dplyr gridExtra stringr stats ggplot2 grDevices MSstatsTMT MSstatsConvert MSstats data.table Rcpp Biostrings checkmate ggrepel BSgenome.Scerevisiae.UCSC.sacCer2: BSgenome GateFinder: splancs mvoutlier methods stats diptest flowCore flowFP lsr: graphics grDevices methods stats BSgenome.Scerevisiae.UCSC.sacCer3: BSgenome shinybusy: htmltools shiny jsonlite htmlwidgets mefa: methods minfi: methods BiocGenerics GenomicRanges SummarizedExperiment Biostrings bumphunter S4Vectors GenomeInfoDb Biobase IRanges beanplot RColorBrewer lattice nor1mix siggenes limma preprocessCore illuminaio DelayedMatrixStats mclust genefilter nlme reshape MASS quadprog data.table GEOquery stats grDevices graphics utils DelayedArray HDF5Array BiocParallel RcppHNSW: methods Rcpp RGSEA: BiocGenerics irlba: Matrix stats methods easyreporting: rmarkdown methods tools shiny rlang varhandle: utils graphics ROC: utils methods knitr phylolm: ape future.apply BSgenome.Ggallus.UCSC.galGal3: BSgenome SingleMoleculeFootprintingData: ExperimentHub utils RANN: CircStats: MASS boot RcppEigen: Matrix Rcpp stats utils Chicago: data.table matrixStats MASS Hmisc Delaporte methods grDevices graphics stats utils foreach: codetools utils iterators dStruct: zoo ggplot2 purrr reshape2 parallel IRanges S4Vectors rlang grDevices stats utils mdp: ggplot2 gridExtra grid stats utils golubEsets: Biobase MANOR: GLAD graphics grDevices stats utils single: Biostrings BiocGenerics dplyr GenomicAlignments IRanges methods reshape2 rlang Rsamtools stats stringr tidyr utils wavethresh: MASS splines2: Rcpp stats RcppArmadillo BSgenome.Ecoli.NCBI.20080805: BSgenome iCNV: CODEX fields ggplot2 truncnorm tidyr data.table dplyr grDevices graphics stats utils rlang shinydashboard: utils shiny htmltools promises RPA: affy BiocGenerics BiocStyle methods rmarkdown phyloseq tLOH: scales stats utils ggplot2 data.table purrr dplyr VariantAnnotation GenomicRanges MatrixGenerics janeaustenr: ScaledMatrix: methods Matrix S4Vectors DelayedArray clipper: Matrix graph methods Biobase Rcpp igraph gRbase qpgraph KEGGgraph corpcor RBGL showimage: png tools ENmix: parallel doParallel foreach SummarizedExperiment stats grDevices graphics preprocessCore matrixStats methods utils geneplotter impute minfi RPMM illuminaio dynamicTreeCut IRanges gtools Biobase ExperimentHub AnnotationHub genefilter gplots quadprog S4Vectors oligo: BiocGenerics oligoClasses Biobase Biostrings affyio affxparser DBI ff graphics methods preprocessCore RSQLite splines stats stats4 utils zlibbioc coGPS: graphics grDevices km.ci: stats survival Rattus.norvegicus: AnnotationDbi methods OrganismDbi GenomicFeatures GO.db org.Rn.eg.db TxDb.Rnorvegicus.UCSC.rn5.refGene OMICsPCA: OMICsPCAdata HelloRanges fpc stats MultiAssayExperiment pdftools methods grDevices utils clValid NbClust cowplot rmarkdown kableExtra rtracklayer IRanges GenomeInfoDb reshape2 ggplot2 factoextra rgl corrplot MASS graphics FactoMineR PerformanceAnalytics tidyr data.table cluster magick mfa: methods stats ggplot2 Rcpp dplyr ggmcmc MCMCpack MCMCglmm coda magrittr tibble Biobase rebus.base: stats scatterHatch: grid ggplot2 plyr spatstat.geom stats grDevices eegc: R.utils gplots sna wordcloud igraph pheatmap edgeR DESeq2 clusterProfiler S4Vectors ggplot2 org.Hs.eg.db org.Mm.eg.db limma DOSE AnnotationDbi RiboProfiling: Biostrings BiocGenerics GenomeInfoDb GenomicRanges IRanges reshape2 GenomicFeatures grid plyr S4Vectors GenomicAlignments ggplot2 ggbio Rsamtools rtracklayer data.table sqldf miRNAmeConverter: miRBaseVersions.db DBI AnnotationDbi reshape2 ANCOMBC: mia stats CVXR DescTools Hmisc MASS Rdpack S4Vectors SingleCellExperiment SummarizedExperiment doParallel doRNG dplyr emmeans energy foreach lme4 lmerTest magrittr nloptr parallel rlang 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purrr MASS pscl assertthat caTools dplyr pheatmap reshape2 corrplot grDevices graphics stats utils data.table R.utils nuCpos: graphics methods GenomicInteractions: InteractionSet Rsamtools rtracklayer GenomicRanges IRanges BiocGenerics data.table stringr GenomeInfoDb ggplot2 grid gridExtra methods igraph S4Vectors dplyr Gviz Biobase graphics stats utils grDevices ChIPanalyser: GenomicRanges Biostrings BSgenome RcppRoll parallel methods IRanges S4Vectors grDevices graphics stats utils rtracklayer ROCR BiocManager GenomeInfoDb strawr: Rcpp ELMER.data: GenomicRanges altcdfenvs: methods BiocGenerics S4Vectors Biobase affy makecdfenv Biostrings hypergraph MethCP: methods utils stats S4Vectors bsseq DSS methylKit DNAcopy GenomicRanges IRanges GenomeInfoDb BiocParallel a4Reporting: methods xtable tokenizers: stringi Rcpp SnowballC concaveman: V8 sf magrittr jsonlite dplyr epimutacions: epimutacionsData minfi bumphunter isotree robustbase ggplot2 GenomicRanges GenomicFeatures IRanges SummarizedExperiment stats matrixStats BiocGenerics S4Vectors utils biomaRt BiocParallel whisker: TarSeqQC: methods GenomicRanges Rsamtools ggplot2 plyr openxlsx grDevices stats utils S4Vectors IRanges BiocGenerics reshape2 GenomeInfoDb BiocParallel Biostrings cowplot graphics GenomicAlignments Hmisc warp: ggridges: ggplot2 grid scales withr PWMEnrich.Hsapiens.background: methods PWMEnrich excluderanges: filelock: ClusterSignificance: methods pracma princurve scatterplot3d RColorBrewer grDevices graphics utils stats betareg: graphics grDevices methods stats flexmix Formula lmtest modeltools sandwich strucchange: zoo sandwich graphics stats utils miRBaseConverter: stats CNEr: Biostrings DBI RSQLite GenomeInfoDb GenomicRanges rtracklayer XVector GenomicAlignments methods S4Vectors IRanges readr BiocGenerics tools parallel reshape2 ggplot2 poweRlaw annotate GO.db R.utils KEGGREST BicARE: Biobase multtest GSEABase maPredictDSC: MASS affy limma gcrma ROC class e1071 caret hgu133plus2.db 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basecallQC: stats utils methods rmarkdown knitr prettydoc yaml ggplot2 stringr XML raster dplyr data.table tidyr magrittr DT lazyeval ShortRead flowViz: flowCore lattice stats4 Biobase graphics grDevices grid KernSmooth latticeExtra MASS methods RColorBrewer stats utils hexbin IDPmisc smoother: TTR HELP: stats graphics grDevices Biobase methods gitcreds: jsonlite: methods SeqGate: S4Vectors SummarizedExperiment GenomicRanges stats methods BiocManager YAPSA: GenomicRanges ggplot2 grid limSolve SomaticSignatures VariantAnnotation GenomeInfoDb reshape2 gridExtra corrplot dendextend GetoptLong circlize gtrellis doParallel PMCMRplus ggbeeswarm ComplexHeatmap KEGGREST grDevices Biostrings BSgenome.Hsapiens.UCSC.hg19 magrittr pracma dplyr utils bc3net: c3net infotheo igraph Matrix lattice MesKit: methods data.table Biostrings dplyr tidyr ape ggrepel pracma ggridges AnnotationDbi IRanges circlize cowplot mclust phangorn ComplexHeatmap ggplot2 RColorBrewer grDevices stats utils S4Vectors lumi: 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httr KEGGREST bookdown HilbertVis: grid lattice ternarynet: utils igraph methods graphics stats BiocParallel shinytoastr: shiny RcisTarget.hg19.motifDBs.cisbpOnly.500bp: data.table MethylSeekR: rtracklayer parallel mhsmm IRanges BSgenome GenomicRanges geneplotter graphics grDevices stats utils ROCit: stats graphics utils methods humanCHRLOC: monaLisa: methods stats utils grDevices graphics BiocGenerics GenomicRanges TFBSTools Biostrings IRanges stabs BSgenome glmnet S4Vectors SummarizedExperiment BiocParallel grid circlize ComplexHeatmap XVector GenomeInfoDb tools vioplot CEMiTool: methods scales dplyr data.table 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 yeast2.db: methods AnnotationDbi org.Sc.sgd.db adabag: rpart caret foreach doParallel viper: Biobase methods mixtools stats parallel e1071 KernSmooth GAprediction: glmnet stats utils Matrix ChromSCape: shiny colourpicker shinyjs rtracklayer shinyFiles shinyhelper shinyWidgets shinydashboardPlus shinycssloaders Matrix plotly shinydashboard colorRamps kableExtra viridis batchelor BiocParallel parallel Rsamtools ggplot2 ggrepel gggenes gridExtra qualV stringdist fs qs DT scran scater ConsensusClusterPlus Rtsne dplyr tidyr GenomicRanges IRanges irlba rlist umap tibble methods jsonlite edgeR stats graphics grDevices utils S4Vectors SingleCellExperiment SummarizedExperiment msigdbr forcats Rcpp coop matrixTests DelayedArray cosmosR: CARNIVAL dorothea dplyr GSEABase igraph progress purrr rlang stringr utils visNetwork DEqMS: graphics stats ggplot2 matrixStats limma minqa: Rcpp dearseq: CompQuadForm dplyr ggplot2 KernSmooth magrittr matrixStats methods patchwork parallel pbapply reshape2 rlang stats statmod survey tibble viridisLite RMassBankData: timeSeries: timeDate graphics grDevices stats utils methods biocGraph: Rgraphviz graph geneplotter BiocGenerics 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SummarizedExperiment methods stats dplyr tibble ggplot2 tidyr GGPA: stats methods graphics GGally network sna scales matrixStats Rcpp RcppArmadillo Cormotif: affy limma graphics grDevices geneLenDataBase: utils rtracklayer GenomicFeatures Dune: BiocParallel SummarizedExperiment utils ggplot2 dplyr tidyr RColorBrewer magrittr gganimate purrr aricode dgof: wppi: dplyr igraph logger methods magrittr Matrix OmnipathR progress purrr rlang RCurl stats tibble tidyr multiOmicsViz: methods parallel doParallel foreach grDevices graphics utils SummarizedExperiment stats Homo.sapiens: AnnotationDbi methods OrganismDbi GenomicFeatures GO.db org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene GNET2: ggplot2 xgboost Rcpp reshape2 grid DiagrammeR methods stats matrixStats graphics SummarizedExperiment dplyr igraph grDevices utils pd.mapping50k.xba240: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors spkTools: Biobase graphics grDevices gtools methods RColorBrewer stats utils robustbase: 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graphics stats utils MsFeatures: methods ProtGenerics MsCoreUtils SummarizedExperiment stats ontologyIndex: GlobalAncova: methods corpcor globaltest annotate AnnotationDbi Biobase dendextend GSEABase VGAM RLHub: AnnotationHub ExperimentHub utils Onassis: rJava OnassisJavaLibs GEOmetadb RSQLite data.table methods tools utils AnnotationDbi RCurl stats DT knitr Rtsne dendextend clusteval ggplot2 ggfortify TxDb.Celegans.UCSC.ce11.ensGene: GenomicFeatures AnnotationDbi motifmatchr: Matrix Rcpp methods TFBSTools Biostrings BSgenome S4Vectors SummarizedExperiment GenomicRanges IRanges Rsamtools GenomeInfoDb RcppArmadillo illuminaio: base64 knitrBootstrap: knitr rmarkdown markdown RedeR: methods igraph COCOA: GenomicRanges BiocGenerics S4Vectors IRanges data.table ggplot2 Biobase stats methods ComplexHeatmap MIRA tidyr grid grDevices simpleCache fitdistrplus methInheritSim: methylKit GenomicRanges GenomeInfoDb parallel BiocGenerics S4Vectors methods stats IRanges msm MatrixGenerics: 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methods BiocGenerics S4Vectors utils stats shiny shinydashboard shinyAce shinyjs DT rintrojs ggplot2 ggrepel colourpicker igraph vipor mgcv graphics grDevices viridisLite shinyWidgets ComplexHeatmap circlize grid multicool: methods Rcpp biodbMirbase: biodb R6 stringr chk RCAS: plotly DT data.table GenomicRanges IRanges BSgenome BSgenome.Hsapiens.UCSC.hg19 GenomeInfoDb Biostrings rtracklayer GenomicFeatures rmarkdown genomation knitr BiocGenerics S4Vectors plotrix pbapply RSQLite proxy pheatmap ggplot2 cowplot ggseqlogo utils ranger gprofiler2 comapr: methods ggplot2 reshape2 dplyr gridExtra plotly circlize rlang GenomicRanges IRanges foreach BiocParallel GenomeInfoDb scales RColorBrewer tidyr S4Vectors utils Matrix grid stats SummarizedExperiment plyr Gviz xtable: stats utils oligoData: oligo UniProt.ws: methods utils RSQLite BiocGenerics AnnotationDbi BiocFileCache cellxgenedp jsonlite httr httpcache progress geneplotter: methods Biobase BiocGenerics lattice annotate AnnotationDbi 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shinycssloaders shinydashboard stats stringr SummarizedExperiment tidyr utils maps: graphics utils tissueTreg: MGFR: biomaRt annotate EnsDb.Mmusculus.v79: ensembldb TeachingDemos: netDx: ROCR pracma ggplot2 glmnet igraph reshape2 parallel stats utils MultiAssayExperiment graphics grDevices methods BiocFileCache GenomicRanges bigmemory doParallel foreach combinat rappdirs GenomeInfoDb S4Vectors IRanges RColorBrewer Rtsne httr plotrix affxparser: xopen: processx MutationalPatterns: GenomicRanges NMF stats S4Vectors BiocGenerics BSgenome VariantAnnotation dplyr tibble purrr tidyr stringr magrittr ggplot2 pracma IRanges GenomeInfoDb Biostrings ggdendro cowplot ggalluvial RColorBrewer methods brglm: profileModel flextable: stats utils grDevices graphics officer rmarkdown knitr htmltools xml2 data.table uuid gdtools rlang base64enc grid schex: SingleCellExperiment Seurat ggplot2 shiny hexbin stats methods cluster dplyr entropy ggforce scales grid concaveman m6Aboost: S4Vectors adabag GenomicRanges dplyr rtracklayer BSgenome Biostrings utils methods IRanges ExperimentHub dirmult: FDb.UCSC.tRNAs: GenomicFeatures AnnotationDbi MIMOSA: MASS plyr reshape Biobase ggplot2 methods Formula data.table pracma MCMCpack coda modeest testthat Rcpp scales dplyr tidyr rlang RcppArmadillo RLMM: graphics grDevices MASS stats utils GA4GHclient: S4Vectors BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges httr IRanges jsonlite methods VariantAnnotation VaSP: ballgown IRanges GenomicRanges S4Vectors parallel matrixStats GenomicAlignments GenomeInfoDb Rsamtools cluster stats graphics methods SpatialDecon: grDevices stats utils graphics SeuratObject Biobase GeomxTools repmis methods Matrix lmtest: stats zoo graphics pasillaBamSubset: dotCall64: org.Ce.eg.db: methods AnnotationDbi emojifont: ggplot2 proto showtext sysfonts utils ExperimentSubset: SummarizedExperiment SingleCellExperiment SpatialExperiment TreeSummarizedExperiment methods Matrix S4Vectors tools: Rgraphviz: methods 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IRanges lifecycle limma magrittr matrixStats methods MultiAssayExperiment purrr R6 Rdpack rlang stats S4Vectors tidyr utils topdownrdata: topdownr parallelMap: BBmisc checkmate parallel stats utils scales: farver labeling lifecycle munsell R6 RColorBrewer rlang viridisLite statTarget: randomForest plyr pdist ROC utils grDevices graphics rrcov stats pls impute Rtpca: stats dplyr tidyr Biobase methods ggplot2 pROC fdrtool splines utils tibble randtests: scoreInvHap: Biostrings methods snpStats VariantAnnotation GenomicRanges BiocParallel graphics SummarizedExperiment ReactomePA: AnnotationDbi DOSE enrichplot ggplot2 ggraph reactome.db igraph graphite miRcompData: utils marr: Rcpp SummarizedExperiment utils methods ggplot2 dplyr magrittr rlang S4Vectors RcppAlgos: gmp methods cpp11 phateR: Matrix methods stats graphics reticulate ggplot2 memoise periodicDNA: Biostrings GenomicRanges IRanges BSgenome BiocParallel S4Vectors rtracklayer stats GenomeInfoDb magrittr zoo ggplot2 methods parallel cowplot BiocGenerics: methods utils graphics stats RLSeq: dplyr ggplot2 RColorBrewer grid regioneR valr caretEnsemble GenomicFeatures rtracklayer GenomicRanges GenomeInfoDb ComplexHeatmap AnnotationHub VennDiagram callr circlize ggplotify ggprism methods stats RLHub aws.s3 pheatmap TOAST: EpiDISH limma nnls quadprog stats methods SummarizedExperiment corpcor doParallel parallel ggplot2 tidyr GGally HDInterval: PAST: stats utils dplyr rlang iterators parallel foreach doParallel qvalue rtracklayer ggplot2 GenomicRanges S4Vectors MLInterfaces: Rcpp methods BiocGenerics Biobase annotate cluster gdata pls sfsmisc MASS rpart genefilter fpc ggvis shiny gbm RColorBrewer hwriter threejs mlbench stats4 tools grDevices graphics stats magrittr MBAmethyl: BLMA: ROntoTools GSA PADOG limma graph stats utils parallel Biobase metafor methods nor1mix: stats graphics proxyC: methods Matrix Rcpp RcppParallel RcppArmadillo Harshlight: affy altcdfenvs Biobase stats utils nullranges: stats IRanges 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emdbook: MASS lattice plyr coda bbmle IgGeneUsage: methods Rcpp SummarizedExperiment StanHeaders rstan reshape2 sqldf: gsubfn proto RSQLite DBI chron biodbExpasy: biodb R6 stringr chk lavaan: methods stats4 stats utils graphics MASS mnormt pbivnorm numDeriv sparseDOSSA: stats utils optparse MASS tmvtnorm MCMCpack irr: lpSolve Modstrings: Biostrings methods BiocGenerics GenomicRanges S4Vectors IRanges XVector stringi stringr crayon grDevices distill: base64enc bookdown digest downlit htmltools jsonlite knitr lubridate mime openssl png rmarkdown rprojroot rstudioapi stats stringr tools utils whisker xfun xml2 yaml tensorA: stats bnstruct: bitops igraph methods keras: generics reticulate tensorflow tfruns magrittr zeallot glue methods R6 ellipsis rlang pathview: KEGGgraph XML Rgraphviz graph png AnnotationDbi org.Hs.eg.db KEGGREST methods utils InteractiveComplexHeatmap: ComplexHeatmap grDevices stats shiny grid GetoptLong S4Vectors digest IRanges kableExtra utils svglite htmltools clisymbols jsonlite RColorBrewer fontawesome plasmodiumanophelescdf: utils AnnotationDbi MEDME: grDevices graphics methods stats utils Biostrings MASS drc lifecycle: cli glue rlang arrayQuality: graphics grDevices grid gridBase hexbin limma marray methods RColorBrewer stats utils sparseMatrixStats: MatrixGenerics Rcpp Matrix matrixStats methods factoextra: ggplot2 abind cluster dendextend FactoMineR ggpubr grid stats reshape2 ggrepel tidyr epiR: survival BiasedUrn pander methods sf lubridate zoo flextable officer zinbwave: methods SummarizedExperiment SingleCellExperiment BiocParallel softImpute stats genefilter edgeR Matrix BioMVCClass: methods MVCClass Biobase graph Rgraphviz directPA: grDevices graphics stats plotly calibrate tofsims: methods utils ProtGenerics Rcpp ALS alsace signal KernSmooth graphics grDevices stats RcppArmadillo igraph: methods graphics grDevices magrittr Matrix pkgconfig rlang stats utils nnls: arrayhelpers: methods utils svUnit weaver: digest tools utils codetools affydata: affy methods borealis: Biobase doParallel snow purrr plyr foreach gamlss gamlss.dist bsseq methods DSS R.utils utils stats ggplot2 cowplot dplyr rlang GenomicRanges networkD3: htmlwidgets igraph magrittr quantsmooth: quantreg grid lumiBarnes: Biobase lumi DEsubs: locfit graph igraph RBGL circlize limma edgeR EBSeq NBPSeq stats grDevices graphics pheatmap utils ggplot2 Matrix jsonlite tools DESeq2 methods textclean: data.table english glue lexicon mgsub qdapRegex stringi textshape utils BioMark: pls glmnet MASS st receptLoss: dplyr ggplot2 magrittr tidyr SummarizedExperiment RandomWalkRestartMH: igraph Matrix dnet methods mAPKL: Biobase multtest clusterSim apcluster limma e1071 AnnotationDbi methods parmigene igraph reactome.db clusterProfiler: AnnotationDbi downloader DOSE dplyr enrichplot GO.db GOSemSim magrittr methods plyr qvalue rlang stats tidyr utils yulab.utils compositions: methods utils grDevices stats tensorA robustbase bayesm graphics MASS airpart: SingleCellExperiment SummarizedExperiment S4Vectors scater stats smurf apeglm emdbook mclust clue dynamicTreeCut matrixStats dplyr plyr ggplot2 ComplexHeatmap forestplot RColorBrewer rlang lpSolve grid grDevices graphics utils pbapply hmdbQuery: XML S4Vectors methods utils MGLM: methods stats parallel stats4 PERFect: sn ggplot2 phyloseq zoo psych stats Matrix fitdistrplus parallel BioCor: BiocParallel GSEABase Matrix methods mathjaxr: agricolae: klaR MASS nlme cluster AlgDesign graphics midasHLA: MultiAssayExperiment assertthat broom dplyr formattable HardyWeinberg kableExtra knitr magrittr methods stringi rlang S4Vectors stats SummarizedExperiment tibble utils qdapTools servr: mime httpuv xfun jsonlite COMPASS: methods Rcpp data.table RColorBrewer scales grid plyr knitr abind clue grDevices utils pdist magrittr reshape2 dplyr tidyr rlang BiocStyle rmarkdown foreach coda GenVisR: methods AnnotationDbi biomaRt BiocGenerics Biostrings DBI FField GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales viridis data.table BSgenome GenomeInfoDb VariantAnnotation phosphonormalizer: plyr stats graphics matrixStats methods tidyHeatmap: methods stats utils dplyr magrittr tidyr rlang purrr tibble ComplexHeatmap viridis circlize RColorBrewer grid grDevices lifecycle dendextend patchwork ALL: Biobase purrr: magrittr rlang SplicingGraphs: GenomicFeatures GenomicAlignments Rgraphviz methods utils graphics igraph BiocGenerics S4Vectors BiocParallel IRanges GenomeInfoDb GenomicRanges Rsamtools graph swamp: impute amap gplots MASS methods kriging: CONSTANd: strandCheckR: dplyr magrittr GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools S4Vectors grid BiocGenerics ggplot2 reshape2 stats gridExtra TxDb.Hsapiens.UCSC.hg38.knownGene methods stringr rmarkdown ALS: nnls Iso msgps: biganalytics: stats utils bigmemory foreach biglm Rcpp BH MsBackendMassbank: Spectra BiocParallel S4Vectors IRanges methods ProtGenerics MsCoreUtils 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AnnotationDbi stopwords: ISOcodes ANF: igraph Biobase survival MASS stats RColorBrewer pwrEWAS: shinyBS foreach doParallel abind truncnorm CpGassoc shiny ggplot2 parallel shinyWidgets BiocManager doSNOW limma genefilter stats grDevices methods utils graphics pwrEWAS.data alevinQC: rmarkdown tools methods ggplot2 GGally dplyr rjson shiny shinydashboard DT stats utils tximport cowplot rlang Rcpp cyanoFilter: Biobase flowCore flowDensity flowClust cytometree ggplot2 GGally graphics grDevices methods mrfDepth stats utils celldex: SummarizedExperiment utils ExperimentHub AnnotationHub AnnotationDbi S4Vectors DelayedArray DelayedMatrixStats GenSA: future: digest globals listenv parallel parallelly tools utils ComplexHeatmap: methods grid graphics stats grDevices circlize GetoptLong colorspace clue RColorBrewer GlobalOptions png digest IRanges matrixStats foreach doParallel codetools SIMAT: Rcpp mzR ggplot2 grid reshape2 grDevices stats utils qpcrNorm: methods Biobase limma affy TPP2D: stats utils dplyr methods ggplot2 tidyr foreach doParallel openxlsx stringr RCurl parallel MASS BiocParallel limma TxDb.Hsapiens.UCSC.hg18.knownGene: GenomicFeatures AnnotationDbi SpikeIn: affy soGGi: BiocGenerics SummarizedExperiment methods reshape2 ggplot2 S4Vectors IRanges GenomeInfoDb GenomicRanges Biostrings Rsamtools GenomicAlignments rtracklayer preprocessCore chipseq BiocParallel R.matlab: methods utils R.methodsS3 R.oo R.utils Mus.musculus: AnnotationDbi methods OrganismDbi GenomicFeatures GO.db org.Mm.eg.db TxDb.Mmusculus.UCSC.mm10.knownGene moanin: SummarizedExperiment topGO stats S4Vectors MASS limma viridis edgeR graphics methods grDevices reshape2 NMI zoo ClusterR splines matrixStats Rfastp: Rcpp rjson ggplot2 reshape2 Rhtslib zlibbioc TileDBArray: DelayedArray methods Rcpp tiledb S4Vectors contiBAIT: BH Rsamtools data.table grDevices clue cluster gplots BiocGenerics S4Vectors IRanges GenomicRanges Rcpp TSP GenomicFiles gtools rtracklayer BiocParallel DNAcopy colorspace reshape2 ggplot2 methods exomeCopy GenomicAlignments diagram lazyeval: KBoost: stats utils metahdep: methods PFAM.db: methods AnnotationDbi Qtlizer: httr curl GenomicRanges stringi ARRmData: polyester: Biostrings IRanges S4Vectors logspline limma zlibbioc divergence: SummarizedExperiment RefManageR: xml2 jsonlite utils plyr tools httr lubridate stringr methods bibtex diffHic: GenomicRanges InteractionSet SummarizedExperiment Rsamtools Rhtslib Biostrings BSgenome rhdf5 edgeR limma csaw locfit methods IRanges S4Vectors GenomeInfoDb BiocGenerics grDevices graphics stats utils Rcpp rtracklayer zlibbioc pepStat: Biobase IRanges limma fields GenomicRanges ggplot2 plyr tools methods data.table SpatialTools: spBayes Rcpp RcppArmadillo GEOsubmission: affy Biobase utils GSEAlm: Biobase healthyFlowData: flowCore methods cytometree: Rcpp ggplot2 graphics igraph mclust methods stats cowplot GoFKernel RcppArmadillo GEOmetadb: GEOquery RSQLite RUnit: utils methods graphics webutils: curl jsonlite BioTIP: igraph cluster psych stringr GenomicRanges MASS scran Rsamtools: methods GenomeInfoDb GenomicRanges Biostrings utils BiocGenerics S4Vectors IRanges XVector zlibbioc bitops BiocParallel stats Rhtslib ChemmineOB: methods BiocGenerics zlibbioc Rcpp BH ATACseqQC: BiocGenerics S4Vectors BSgenome Biostrings ChIPpeakAnno IRanges GenomicRanges GenomicAlignments GenomeInfoDb GenomicScores graphics grid limma Rsamtools randomForest rtracklayer stats motifStack preseqR utils KernSmooth edgeR sets: graphics grDevices stats utils GOexpress: grid stats graphics Biobase biomaRt stringr ggplot2 RColorBrewer gplots randomForest RCurl glue: methods clusterRepro: a4Preproc: BiocGenerics Biobase shinyepico: DT data.table doParallel dplyr foreach GenomicRanges ggplot2 gplots heatmaply limma minfi plotly reshape2 rlang rmarkdown rtracklayer shiny shinyWidgets shinycssloaders shinyjs shinythemes statmod tidyr zip PolyPhen.Hsapiens.dbSNP131: VariantAnnotation RSQLite AnnotationDbi org.Xl.eg.db: methods AnnotationDbi APL: reticulate ggrepel ggplot2 viridisLite plotly Seurat SingleCellExperiment magrittr SummarizedExperiment topGO methods stats utils org.Hs.eg.db org.Mm.eg.db rlang forcats: cli ellipsis glue lifecycle magrittr rlang tibble withr TADCompare: dplyr PRIMME cluster Matrix magrittr HiCcompare ggplot2 tidyr ggpubr RColorBrewer reshape2 cowplot genomeIntervals: methods intervals BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors CGHbase: methods Biobase marray CAMERA: methods Biobase xcms RBGL graph graphics grDevices stats utils Hmisc igraph PhenStat: SmoothWin methods car nlme nortest MASS msgps logistf knitr tools pingr ggplot2 reshape corrplot graph lme4 graphics grDevices utils stats dixonTest: BAC: pbapply: parallel methylclock: methylclockData devtools quadprog Rcpp ExperimentHub dplyr impute PerformanceAnalytics Biobase ggpmisc tidyverse ggplot2 ggpubr minfi tibble RPMM stats graphics tidyr gridExtra preprocessCore dynamicTreeCut planet genotypeeval: VariantAnnotation ggplot2 rtracklayer BiocGenerics GenomicRanges GenomeInfoDb IRanges methods BiocParallel graphics stats qdapRegex: stringi ndexr: igraph RCX httr jsonlite plyr tidyr sylly: methods martini: igraph Matrix methods Rcpp snpStats stats utils RcppEigen TxDb.Hsapiens.UCSC.hg19.knownGene: GenomicFeatures AnnotationDbi ewceData: ExperimentHub mirbase.db: methods AnnotationDbi dasper: basilisk BiocFileCache BiocParallel data.table dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel grid IRanges magrittr megadepth methods plyranges readr reticulate rtracklayer S4Vectors stringr SummarizedExperiment tidyr apeglm: emdbook SummarizedExperiment GenomicRanges methods stats utils Rcpp RcppEigen RcppNumerical gpaExample: ChIPseeker: AnnotationDbi BiocGenerics boot enrichplot IRanges GenomeInfoDb GenomicRanges GenomicFeatures ggplot2 ggVennDiagram gplots graphics grDevices gtools methods plotrix dplyr parallel magrittr RColorBrewer rtracklayer S4Vectors stats TxDb.Hsapiens.UCSC.hg19.knownGene utils treemap: colorspace data.table ggplot2 grid gridBase igraph methods RColorBrewer shiny stepNorm: marray methods MASS stats RcppThread: gghalves: ggplot2 grid gtable grDevices R.oo: R.methodsS3 methods utils threejs: igraph htmlwidgets base64enc crosstalk methods stats CONFESS: grDevices utils stats graphics methods changepoint cluster contrast data.table ecp EBImage flexmix flowCore flowClust flowMeans flowMerge flowPeaks foreach ggplot2 grid limma MASS moments outliers parallel plotrix raster readbitmap reshape2 SamSPECTRAL waveslim wavethresh zoo FilterFFPE: foreach doParallel GenomicRanges IRanges Rsamtools parallel S4Vectors SPONGE: Biobase stats ppcor logging foreach doRNG data.table MASS expm gRbase glmnet igraph iterators tidyverse caret dplyr biomaRt randomForest ggridges cvms miRBaseConverter ComplexHeatmap ggplot2 MetBrewer rlang tnet ggpubr stringr tidyr SeqGSEA: Biobase doParallel DESeq2 methods biomaRt FoldGO: topGO ggplot2 tidyr stats methods mAPKLData: Cepo: GSEABase DelayedMatrixStats DelayedArray HDF5Array S4Vectors methods SingleCellExperiment SummarizedExperiment ggplot2 rlang grDevices patchwork reshape2 BiocParallel stats dplyr PFP: graph igraph KEGGgraph clusterProfiler ggplot2 plyr tidyr magrittr stats methods utils mpra: methods BiocGenerics SummarizedExperiment limma S4Vectors scales stats graphics statmod MsBackendMsp: Spectra BiocParallel S4Vectors IRanges MsCoreUtils methods stats IlluminaHumanMethylationEPICanno.ilm10b4.hg19: minfi gtrellis: grid IRanges GenomicRanges circlize GetoptLong grDevices utils BiasedUrn: chromPlot: stats utils graphics grDevices datasets base biomaRt GenomicRanges tidydr: ggplot2 grid rlang utils pspline: stats graphics BrainSABER: biomaRt SummarizedExperiment data.table lsa methods S4Vectors utils BiocFileCache shiny C50: partykit Cubist MLSeq: caret ggplot2 testthat VennDiagram pamr methods DESeq2 edgeR limma Biobase SummarizedExperiment plyr foreach utils sSeq xtable scico: scales grDevices cellmigRation: methods foreach tiff graphics stats utils reshape2 parallel doParallel grDevices matrixStats FME SpatialTools sp vioplot FactoMineR Hmisc gridExtra: gtable grid grDevices graphics utils proBAMr: IRanges AnnotationDbi GenomicRanges Biostrings GenomicFeatures rtracklayer biovizBase: methods grDevices stats scales Hmisc RColorBrewer dichromat BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges SummarizedExperiment Biostrings Rsamtools GenomicAlignments GenomicFeatures AnnotationDbi VariantAnnotation ensembldb AnnotationFilter rlang seqPattern: methods Biostrings GenomicRanges IRanges KernSmooth plotrix pd.huex.1.0.st.v2: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors bigrquery: assertthat bit64 curl DBI gargle glue httr lifecycle jsonlite methods prettyunits progress Rcpp rlang tibble rapidjsonr TBSignatureProfiler: ASSIGN BiocGenerics BiocParallel ComplexHeatmap DESeq2 DT edgeR gdata ggplot2 GSVA magrittr methods 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singleCellTK: SummarizedExperiment SingleCellExperiment DelayedArray Biobase ape batchelor BiocParallel celldex colourpicker colorspace cowplot cluster ComplexHeatmap data.table DelayedMatrixStats DESeq2 dplyr DT ExperimentHub fields ggplot2 ggplotify ggrepel ggtree gridExtra GSVA GSVAdata igraph KernSmooth limma MAST Matrix matrixStats methods msigdbr multtest plotly plyr ROCR Rtsne S4Vectors scater scMerge scran Seurat shiny shinyjs SingleR SoupX sva reshape2 shinyalert circlize enrichR celda shinycssloaders DropletUtils scds reticulate tools tximport fishpond withr GSEABase R.utils zinbwave scRNAseq TENxPBMCData yaml rmarkdown magrittr scDblFinder metap VAM tibble rlang TSCAN TrajectoryUtils generics scuttle utils stats BubbleTree: IRanges GenomicRanges plyr dplyr magrittr BiocGenerics BiocStyle Biobase ggplot2 WriteXLS gtools RColorBrewer limma grid gtable gridExtra biovizBase e1071 methods grDevices stats utils corral: ggplot2 ggthemes grDevices gridExtra irlba Matrix methods 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HDF5Array mclust: stats utils graphics grDevices OSAT: methods stats EpiTxDb.Hs.hg38: AnnotationHub EpiTxDb BSgenome.Drerio.UCSC.danRer7: BSgenome rprimer: Biostrings bslib DT ggplot2 IRanges mathjaxr methods patchwork reshape2 S4Vectors shiny shinycssloaders shinyFeedback rmspc: processx BiocManager rtracklayer stats tools methods GenomicRanges stringr Rmagic: Matrix methods stats reticulate ggplot2 yeastNagalakshmi: ABarray: Biobase graphics grDevices methods multtest stats tcltk utils vdiffr: diffobj glue grDevices htmltools lifecycle rlang testthat xml2 cpp11 anocva: cluster consensusOV: Biobase GSVA gdata genefu limma matrixStats randomForest stats utils methods TypeInfo: methods evaluate: methods BBCAnalyzer: SummarizedExperiment VariantAnnotation Rsamtools grDevices GenomicRanges IRanges Biostrings copula: stats graphics methods stats4 Matrix lattice colorspace gsl ADGofTest stabledist mvtnorm pcaPP pspline numDeriv GSAR: igraph stats graphics RNAmodR.ML: RNAmodR methods BiocGenerics S4Vectors IRanges GenomicRanges stats ranger sparrow: babelgene BiocGenerics BiocParallel BiocSet checkmate circlize ComplexHeatmap data.table DelayedMatrixStats edgeR ggplot2 graphics grDevices GSEABase irlba limma Matrix methods plotly stats utils viridis sparseinv: Matrix methods Rcpp spam lmerTest: lme4 stats methods numDeriv MASS ggplot2 eudysbiome: plyr Rsamtools R.utils Biostrings DelayedArray: methods stats4 Matrix BiocGenerics MatrixGenerics S4Vectors IRanges stats gridtext: curl grid grDevices markdown rlang Rcpp png jpeg stringr xml2 pd.genomewidesnp.5: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors pd.genomewidesnp.6: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors BHC: rBiopaxParser: data.table XML plgem: utils Biobase MASS methods assertive.datetimes: assertive.base assertive.types EBSeqHMM: EBSeq GSCA: shiny sp gplots ggplot2 reshape2 RColorBrewer rhdf5 graphics BioPlex: SummarizedExperiment BiocFileCache GenomicRanges GenomeInfoDb GEOquery graph methods utils xts: zoo methods RPostgreSQL: methods DBI IlluminaHumanMethylation450kmanifest: minfi fmcsR: ChemmineR methods RUnit BiocGenerics parallel GeneExpressionSignature: Biobase stats methods arrayMvout: tools methods utils parody Biobase affy mdqc affyContam lumi drosophila2probe: AnnotationDbi BUSseq: SingleCellExperiment SummarizedExperiment S4Vectors gplots grDevices methods stats utils xmapbridge: methods EmpiricalBrownsMethod: biodbKegg: R6 biodb chk lifecycle HelloRangesData: RhpcBLASctl: seqsetvis: ggplot2 cowplot data.table eulerr GenomeInfoDb GenomicAlignments GenomicRanges ggplotify grDevices grid IRanges limma methods pbapply pbmcapply png RColorBrewer Rsamtools rtracklayer S4Vectors stats UpSetR biocthis: BiocManager fs glue rlang styler usethis PMA: flowClean: flowCore bit changepoint sfsmisc ChIC: spp ChIC.data caTools methods GenomicRanges IRanges parallel progress randomForest caret grDevices stats utils graphics 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methods rlang utils Biostrings stats SummarizedExperiment ellipse: graphics stats epigenomix: methods Biobase S4Vectors IRanges GenomicRanges SummarizedExperiment BiocGenerics MCMCpack Rsamtools parallel GenomeInfoDb beadarray ffpeExampleData: lumi rmarkdown: bslib evaluate htmltools jquerylib jsonlite knitr methods stringr tinytex tools utils xfun yaml mnormt: glmmTMB: methods TMB lme4 Matrix nlme numDeriv RcppEigen BiocNeighbors: Rcpp S4Vectors BiocParallel stats methods Matrix RcppHNSW baySeq: methods GenomicRanges abind parallel edgeR europepmc: httr jsonlite plyr dplyr progress urltools purrr xml2 tibble tidyr rlang bamsignals: methods BiocGenerics Rcpp IRanges GenomicRanges zlibbioc Rhtslib hgu95a.db: methods AnnotationDbi org.Hs.eg.db distances: stats MOGAMUN: stats utils RCy3 stringr graphics grDevices RUnit BiocParallel igraph supraHex: hexbin ape MASS grDevices graphics stats readr tibble tidyr dplyr stringr purrr magrittr igraph methods timecoursedata: SummarizedExperiment netresponse: BiocStyle Rgraphviz rmarkdown methods minet mclust reshape2 ggplot2 graph igraph parallel plyr qvalue RColorBrewer qqman: calibrate spikeLI: graphics grDevices stats utils annotate: AnnotationDbi XML Biobase DBI xtable graphics utils stats methods BiocGenerics httr RTriangle: BiocWorkflowTools: BiocStyle bookdown git2r httr knitr rmarkdown rstudioapi stringr tools utils usethis shinytest: assertthat callr crayon debugme digest htmlwidgets httpuv httr jsonlite parsedate pingr R6 rematch rlang rstudioapi shiny testthat utils webdriver withr WGCNA: dynamicTreeCut fastcluster stats grDevices utils matrixStats Hmisc impute splines foreach doParallel preprocessCore survival parallel GO.db AnnotationDbi Rcpp tricycle: SingleCellExperiment methods circular ggplot2 ggnewscale AnnotationDbi scater GenomicRanges IRanges S4Vectors scattermore dplyr RColorBrewer grDevices stats SummarizedExperiment utils ropls: Biobase graphics grDevices methods stats MultiAssayExperiment MultiDataSet SummarizedExperiment utils VGAM: methods stats stats4 splines ggcorrplot: ggplot2 reshape2 stats FISHalyseR: EBImage abind mCSEAdata: transite: BiocGenerics Biostrings dplyr GenomicRanges ggplot2 ggseqlogo grDevices gridExtra methods parallel Rcpp scales stats TFMPvalue utils meshr: markdown rmarkdown BiocStyle knitr methods stats utils fdrtool MeSHDbi Category S4Vectors BiocGenerics RSQLite BiocIO: BiocGenerics S4Vectors methods tools pdftools: Rcpp qpdf shinycustomloader: glue shiny annotatr: AnnotationDbi AnnotationHub dplyr GenomicFeatures GenomicRanges GenomeInfoDb ggplot2 IRanges methods readr regioneR reshape2 rtracklayer S4Vectors stats utils BANDITS: Rcpp doRNG MASS data.table R.utils doParallel parallel foreach methods stats graphics ggplot2 DRIMSeq BiocParallel RcppArmadillo summarytools: base64enc checkmate dplyr grDevices htmltools lubridate magick matrixStats methods pander pryr rapportools stats tcltk tibble tidyr utils curatedTCGAData: MultiAssayExperiment AnnotationHub ExperimentHub HDF5Array methods S4Vectors stats SummarizedExperiment utils iC10: pamr impute iC10TrainingData reportr: ore cpp11: SLGI: ScISI lattice AnnotationDbi Biobase GO.db graphics methods stats BiocGenerics omicplotR: ALDEx2 compositions DT grDevices knitr jsonlite matrixStats rmarkdown shiny stats vegan zCompositions BMA: survival leaps robustbase inline rrcov methods XCIR: methods stats utils tools data.table Biostrings IRanges VariantAnnotation seqminer ggplot2 biomaRt readxl S4Vectors rstatix: stats utils tidyr purrr broom rlang tibble dplyr magrittr corrplot tidyselect car generics lineagespot: VariantAnnotation MatrixGenerics SummarizedExperiment data.table stringr httr utils valr: broom cli dplyr ggplot2 Rcpp readr rlang rtracklayer stringr tibble kernlab: methods stats grDevices graphics yamss: methods BiocGenerics SummarizedExperiment IRanges stats S4Vectors EBImage Matrix mzR data.table grDevices limma SNAGEEdata: metaCCA: ggstance: ggplot2 plyr rlang withr pRolocdata: MSnbase Biobase utils MCMCprecision: Rcpp parallel utils stats Matrix combinat RcppArmadillo RcppProgress RcppEigen ggformula: ggplot2 ggstance scales ggridges mosaicCore rlang magrittr tibble stringr ggforce grid labelled regsplice: glmnet SummarizedExperiment S4Vectors limma edgeR stats pbapply utils methods deco: AnnotationDbi BiocParallel SummarizedExperiment limma stats methods ggplot2 foreign graphics BiocStyle Biobase cluster gplots RColorBrewer locfit made4 ade4 sfsmisc scatterplot3d gdata grDevices utils reshape2 gridExtra ROCpAI: boot SummarizedExperiment fission knitr methods MetaCyto: flowCore tidyr fastcluster ggplot2 metafor cluster FlowSOM grDevices graphics stats utils rmeta: grid stats graphics ProteoDisco: BiocGenerics BiocParallel Biostrings checkmate cleaver dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges methods ParallelLogger plyr rlang S4Vectors tibble tidyr VariantAnnotation XVector repmis: data.table digest httr plyr R.cache shinyBS: shiny htmltools