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methods ggplot2 dplyr magrittr rlang S4Vectors BadRegionFinder: VariantAnnotation Rsamtools biomaRt GenomicRanges S4Vectors utils stats grDevices graphics diceR: abind assertthat class clue clusterSim clv clValid dplyr ggplot2 infotheo klaR magrittr mclust methods NMF purrr RankAggreg Rcpp stringr tidyr yardstick gclus: cluster cBioPortalData: AnVIL MultiAssayExperiment BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges methods readr RaggedExperiment RTCGAToolbox S4Vectors SummarizedExperiment stats tibble tidyr TCGAutils utils RBM: limma marray broom: backports dplyr ellipsis generics glue lifecycle purrr rlang stringr tibble tidyr inline: methods fontLiberation: oncomix: ggplot2 ggrepel RColorBrewer mclust stats SummarizedExperiment shape: stats graphics grDevices logistf: mice mgcv formula.tools Matrix scmeth: knitr rmarkdown bsseq AnnotationHub GenomicRanges reshape2 stats utils BSgenome DelayedArray annotatr SummarizedExperiment GenomeInfoDb Biostrings DT HDF5Array scTHI.data: lgr: R6 GraphAlignment: GeneGeneInteR: snpStats mvtnorm Rsamtools igraph kernlab FactoMineR IRanges GenomicRanges data.table grDevices graphics stats utils methods BSgenome.Mmusculus.UCSC.mm8: BSgenome einsum: Rcpp glue mathjaxr logging: methods nullranges: stats IRanges GenomicRanges GenomeInfoDb methods rlang S4Vectors scales InteractionSet ggplot2 grDevices plyranges data.table progress ggridges BSgenome.Mmusculus.UCSC.mm9: BSgenome mosbi: Rcpp BH xml2 methods igraph fabia RcppParallel biclust isa2 QUBIC akmbiclust RColorBrewer GOfuncR: vioplot Rcpp mapplots gtools GenomicRanges IRanges AnnotationDbi utils grDevices graphics stats enrichplot: aplot DOSE ggnewscale ggfun ggplot2 ggraph graphics grid igraph methods plyr purrr RColorBrewer reshape2 rlang stats utils scatterpie shadowtext GOSemSim magrittr ggtree yulab.utils SCArray: gdsfmt methods DelayedArray S4Vectors utils Matrix BiocParallel DelayedMatrixStats SummarizedExperiment SingleCellExperiment BiocSingular NanoStringNCTools: Biobase S4Vectors ggplot2 BiocGenerics Biostrings ggbeeswarm ggiraph ggthemes grDevices IRanges methods pheatmap RColorBrewer stats utils blimaTestingData: netZooR: igraph reticulate pandaR yarn matrixcalc RCy3 viridisLite STRINGdb Biobase GOstats AnnotationDbi matrixStats GO.db org.Hs.eg.db Matrix gplots nnet data.table vegan stats utils reshape reshape2 penalized parallel doParallel foreach ggplot2 ggdendro grid MASS assertthat tidyr methods dplyr graphics RCM: DBI RColorBrewer alabama edgeR reshape2 tseries stats VGAM ggplot2 nleqslv phyloseq tensor MASS grDevices graphics methods prettyGraphs: EGSEA: Biobase gage AnnotationDbi topGO pathview PADOG GSVA globaltest limma edgeR HTMLUtils hwriter gplots ggplot2 safe stringi parallel stats metap grDevices graphics utils org.Hs.eg.db org.Mm.eg.db org.Rn.eg.db RColorBrewer methods EGSEAdata htmlwidgets plotly DT tfruns: utils jsonlite base64enc yaml config magrittr whisker tidyselect rlang rstudioapi reticulate HDO.db: AnnotationDbi methods utils WGSmapp: GenomicRanges GSAR: igraph stats graphics rentrez: XML httr jsonlite sampleClassifier: MGFM MGFR annotate e1071 ggplot2 stats utils tester: rpart: graphics stats grDevices ggmanh: methods ggplot2 gdsfmt ggrepel grDevices RColorBrewer rlang scales SeqArray stats bbotk: paradox checkmate data.table lgr methods mlr3misc R6 lhs: Rcpp CircSeqAlignTk: stats tools utils methods S4Vectors rlang magrittr dplyr tidyr ggplot2 BiocGenerics Biostrings IRanges ShortRead Rsamtools Rbowtie2 Rhisat2 RCX: jsonlite plyr igraph methods EnvStats: MASS ggplot2 nortest Cairo: grDevices graphics nipals: genomicInstability: checkmate mixtools SummarizedExperiment tinytex: xfun 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 shinycssloaders: digest glue grDevices shiny epivizrServer: methods httpuv R6 rjson mime genomeIntervals: methods intervals BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors GSCA: shiny sp gplots ggplot2 reshape2 RColorBrewer rhdf5 graphics MobilityTransformR: MSnbase xcms MetaboCoreUtils Spectra forecast: colorspace fracdiff generics ggplot2 graphics lmtest magrittr nnet parallel Rcpp stats timeDate tseries urca zoo RcppArmadillo minfiData: minfi IlluminaHumanMethylation450kmanifest IlluminaHumanMethylation450kanno.ilmn12.hg19 ChIC: spp ChIC.data caTools methods GenomicRanges IRanges parallel progress randomForest caret grDevices stats utils graphics S4Vectors BiocGenerics genomeIntervals Rsamtools dpeak: methods stats utils graphics Rcpp MASS IRanges BSgenome grDevices parallel flowCHIC: methods flowCore EBImage vegan hexbin ggplot2 grid DAPAR: Biobase MSnbase DAPARdata utils highcharter foreach tensorA: stats PCAN: BiocParallel grDevices stats Rattus.norvegicus: AnnotationDbi methods OrganismDbi GenomicFeatures GO.db org.Rn.eg.db TxDb.Rnorvegicus.UCSC.rn5.refGene cosmosR: CARNIVAL dorothea dplyr GSEABase igraph progress purrr rlang stringr utils visNetwork ipred: rpart MASS survival nnet class prodlim RNAmodR: S4Vectors IRanges GenomicRanges Modstrings methods stats grDevices matrixStats BiocGenerics Biostrings BiocParallel GenomicFeatures GenomicAlignments GenomeInfoDb rtracklayer Rsamtools BSgenome RColorBrewer colorRamps ggplot2 Gviz reshape2 graphics ROCR rfPred: methods utils GenomeInfoDb data.table IRanges GenomicRanges parallel Rsamtools statebins: ggplot2 scales grid minionSummaryData: myvariant: VariantAnnotation httr jsonlite S4Vectors Hmisc plyr magrittr GenomeInfoDb OSAT: methods stats SNPhoodData: nnls: DBI: methods SOMbrero: igraph markdown scatterplot3d shiny grDevices graphics stats ggplot2 ggwordcloud metR interp biomvRCNS: IRanges GenomicRanges Gviz methods mvtnorm beadarraySNP: methods Biobase quantsmooth BiocFHIR: DT shiny jsonlite graph tidyr visNetwork dplyr utils methods BiocBaseUtils nloptr: testthat mirbase.db: methods AnnotationDbi bacon: methods stats ggplot2 graphics BiocParallel ellipse systemPipeR: Rsamtools Biostrings ShortRead methods GenomicRanges SummarizedExperiment ggplot2 yaml stringr magrittr S4Vectors crayon BiocGenerics htmlwidgets RImmPort: plyr dplyr DBI data.table reshape2 methods sqldf tools utils RSQLite RSVSim: Biostrings GenomicRanges methods IRanges ShortRead org.Ce.eg.db: methods AnnotationDbi RcppHMM: Rcpp RcppArmadillo arrayQuality: graphics grDevices grid gridBase hexbin limma marray methods RColorBrewer stats utils TCGAMethylation450k: ExperimentHub: methods BiocGenerics AnnotationHub BiocFileCache utils S4Vectors BiocManager rappdirs SpikeInSubset: Biobase affy cleaver: methods Biostrings S4Vectors IRanges SigsPack: quadprog methods Biobase BSgenome VariantAnnotation Biostrings GenomeInfoDb GenomicRanges rtracklayer SummarizedExperiment graphics stats utils powerTCR: cubature doParallel evmix foreach magrittr methods parallel purrr stats truncdist vegan VGAM reconsi: phyloseq ks reshape2 ggplot2 stats methods graphics grDevices matrixStats Matrix GCSscore: BiocManager Biobase utils methods RSQLite devtools dplR stringr graphics stats affxparser data.table countsimQC: rmarkdown edgeR DESeq2 dplyr tidyr ggplot2 grDevices tools SummarizedExperiment genefilter DT GenomeInfoDbData caTools randtests stats utils methods ragg EnsDb.Rnorvegicus.v79: ensembldb zoo: stats utils graphics grDevices lattice visNetwork: htmlwidgets htmltools jsonlite magrittr utils methods grDevices stats SIMAT: Rcpp mzR ggplot2 grid reshape2 grDevices stats utils synapterdata: synapter utils WriteXLS: utils git2r: graphics utils highcharter: htmlwidgets magrittr purrr rlist assertthat zoo dplyr tibble stringr broom xts quantmod tidyr htmltools jsonlite igraph lubridate yaml rlang rjson AWFisher: edgeR limma stats survey: grid methods Matrix survival stats graphics splines lattice minqa numDeriv mitools miRNApath: methods epigenomix: methods Biobase S4Vectors IRanges GenomicRanges SummarizedExperiment BiocGenerics MCMCpack Rsamtools parallel GenomeInfoDb beadarray kSamples: SuppDists methods graphics stats gplots: gtools stats caTools KernSmooth methods GSALightning: Matrix data.table stats scrypt: Rcpp bugsigdbr: BiocFileCache methods vroom utils org.Xl.eg.db: methods AnnotationDbi GeneAccord: biomaRt caTools dplyr ggplot2 graphics grDevices gtools ggpubr magrittr maxLik RColorBrewer reshape2 stats tibble utils coRdon: methods stats utils Biostrings Biobase dplyr stringr purrr ggplot2 data.table vegan: permute lattice MASS cluster mgcv oppti: limma stats reshape ggplot2 grDevices RColorBrewer pheatmap knitr methods devtools parallelDist synaptome.db: synaptome.data DBI RSQLite dplyr dbplyr igraph Rdpack AnnotationHub utils RUnit: utils methods graphics InTAD: methods S4Vectors IRanges GenomicRanges MultiAssayExperiment SummarizedExperiment stats BiocGenerics Biobase rtracklayer parallel graphics mclust qvalue ggplot2 utils ggpubr TEKRABber: apeglm biomaRt dplyr DESeq2 magrittr Rcpp SCBN SummarizedExperiment stats utils TOAST: EpiDISH limma nnls quadprog stats methods SummarizedExperiment corpcor doParallel parallel ggplot2 tidyr GGally idiogram: methods Biobase annotate plotrix pd.mapping50k.xba240: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors glue: methods ParallelLogger: snow xml2 jsonlite methods utils DirichletReg: Formula stats graphics methods maxLik snifter: basilisk reticulate irlba stats assertthat ANCOMBC: mia stats CVXR DescTools Hmisc MASS Matrix Rdpack S4Vectors SingleCellExperiment SummarizedExperiment TreeSummarizedExperiment doParallel doRNG energy foreach gtools lme4 lmerTest multcomp nloptr parallel utils 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 RUVSeq: Biobase EDASeq edgeR methods MASS findpython: epistack: GenomicRanges SummarizedExperiment BiocGenerics S4Vectors IRanges graphics plotrix grDevices stats methods CoSIA: methods ExperimentHub dplyr magrittr RColorBrewer tidyr plotly stringr ggplot2 tibble org.Hs.eg.db org.Mm.eg.db org.Dr.eg.db org.Ce.eg.db org.Dm.eg.db org.Rn.eg.db AnnotationDbi biomaRt homologene annotationTools readr tidyselect stats insight: methods stats utils badger: dlstats rvcheck desc usethis PeacoQC: circlize ComplexHeatmap flowCore flowWorkspace ggplot2 grDevices grid gridExtra methods plyr stats utils geneClassifiers: utils methods stats Biobase BiocGenerics timecourse: MASS methods Biobase graphics limma marray stats ITALICS: GLAD ITALICSData oligo affxparser pd.mapping50k.xba240 DBI oligoClasses stats optextras: numDeriv 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 MASS grDevices MCMCprecision: Rcpp parallel utils stats Matrix combinat RcppArmadillo RcppProgress RcppEigen gRain: methods gRbase igraph stats4 broom magrittr Rcpp RcppArmadillo RcppEigen DelayedRandomArray: DelayedArray methods dqrng Rcpp BH ggforce: ggplot2 Rcpp grid scales MASS tweenr gtable rlang polyclip stats grDevices tidyselect withr utils lifecycle cli vctrs systemfonts RcppEigen reprex: callr cli clipr fs glue knitr lifecycle rlang rmarkdown rstudioapi utils withr MOGAMUN: stats utils RCy3 stringr graphics grDevices RUnit BiocParallel igraph kpeaks: graphics stats utils methods GenomicDistributionsData: ExperimentHub AnnotationHub AnnotationFilter data.table utils BSgenome GenomeInfoDb GenomicFeatures GenomicRanges ensembldb EBcoexpress: EBarrays mclust minqa netboxr: igraph parallel RColorBrewer DT stats clusterProfiler data.table gplots jsonlite plyr DFP: methods Biobase tomoda: methods stats grDevices reshape2 Rtsne umap RColorBrewer ggplot2 ggrepel SummarizedExperiment progress: hms prettyunits R6 crayon pd.genomewidesnp.5: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors pd.genomewidesnp.6: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors CoCiteStats: org.Hs.eg.db AnnotationDbi Matrix: methods grDevices graphics grid lattice stats utils pdist: methods sigFeature: biocViews nlme e1071 openxlsx pheatmap RColorBrewer Matrix SparseM graphics stats utils SummarizedExperiment BiocParallel methods devtools: usethis cli desc ellipsis fs lifecycle memoise miniUI pkgbuild pkgdown pkgload profvis rcmdcheck remotes rlang roxygen2 rversions sessioninfo stats testthat tools urlchecker utils withr cycle: Mfuzz Biobase stats bnlearn: methods webmockr: curl jsonlite magrittr R6 urltools fauxpas crul base64enc trio: grDevices graphics methods stats survival utils siggenes LogicReg torch: Rcpp R6 withr rlang methods utils stats bit64 magrittr tools coro callr cli glue ellipsis desc dada2: Rcpp methods Biostrings ggplot2 reshape2 ShortRead RcppParallel parallel IRanges XVector BiocGenerics loo: checkmate matrixStats parallel stats SingleMoleculeFootprintingData: ExperimentHub utils Rtpca: stats dplyr tidyr Biobase methods ggplot2 pROC fdrtool splines utils tibble aws.s3: utils tools curl httr xml2 base64enc digest aws.signature NxtIRFdata: ExperimentHub BiocFileCache rtracklayer R.utils stepNorm: marray methods MASS stats NanoporeRNASeq: ExperimentHub PCHiCdata: Chicago zenith: limma methods variancePartition EnrichmentBrowser GSEABase msigdbr Rfast ggplot2 tidyr reshape2 progress utils Rdpack stats BSgenome.Celegans.UCSC.ce10: BSgenome DepInfeR: matrixStats glmnet stats BiocParallel BSgenome.Celegans.UCSC.ce11: BSgenome DrImpute: Rcpp RcppArmadillo frmaExampleData: ExploreModelMatrix: shiny shinydashboard DT cowplot utils dplyr magrittr tidyr ggplot2 stats methods rintrojs scales tibble MASS limma S4Vectors shinyjs COTAN: stats plyr dplyr methods grDevices Matrix ggplot2 ggrepel ggthemes graphics parallel parallelly tibble tidyr irlba ComplexHeatmap circlize grid scales RColorBrewer utils rlang Rfast stringr Seurat umap factoextra dendextend zeallot assertthat withr EWCE: RNOmni stats utils methods ewceData dplyr ggplot2 reshape2 limma stringr HGNChelper Matrix parallel SingleCellExperiment SummarizedExperiment DelayedArray BiocParallel orthogene data.table biclust: MASS grid colorspace lattice methods flexclust additivityTests tidyr ggplot2 BUScorrect: gplots methods grDevices stats SummarizedExperiment R2jags: rjags abind coda graphics grDevices methods R2WinBUGS parallel stats utils DoubleExpSeq: numDeriv datasets grDevices graphics stats utils waffle: ggplot2 RColorBrewer grid gridExtra gtable extrafont curl stringr stats htmlwidgets DT plyr rlang utils ontologyIndex: awst: stats methods SummarizedExperiment mlr3measures: checkmate PRROC tanggle: ggplot2 ggtree ape phangorn utils methods chromstaR: GenomicRanges ggplot2 chromstaRData methods utils grDevices graphics stats foreach doParallel BiocGenerics S4Vectors GenomeInfoDb IRanges reshape2 Rsamtools GenomicAlignments bamsignals mvtnorm CAGEfightR: GenomicRanges rtracklayer SummarizedExperiment pryr assertthat methods Matrix BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicFeatures GenomicAlignments BiocParallel GenomicFiles Gviz InteractionSet GenomicInteractions flowMap: ade4 doParallel abind reshape2 scales Matrix methods rsample: cli dplyr furrr generics glue lifecycle methods pillar purrr rlang slider tibble tidyr tidyselect vctrs TxDb.Rnorvegicus.UCSC.rn7.refGene: GenomicFeatures AnnotationDbi misc3d: grDevices graphics stats tcltk caret: ggplot2 lattice e1071 foreach grDevices methods ModelMetrics nlme plyr pROC recipes reshape2 stats stats4 utils withr consensusOV: Biobase GSVA gdata genefu limma matrixStats randomForest stats utils methods spatstat: spatstat.data spatstat.geom spatstat.random spatstat.explore spatstat.model spatstat.linnet utils spatstat.utils ismev: mgcv ggtree: ape aplot dplyr ggplot2 grid magrittr methods purrr rlang ggfun yulab.utils tidyr tidytree treeio utils scales stats cli granulator: cowplot e1071 epiR dplyr dtangle ggplot2 ggplotify grDevices limSolve magrittr MASS nnls parallel pheatmap purrr rlang stats tibble tidyr utils scCB2: SingleCellExperiment SummarizedExperiment Matrix methods utils stats edgeR rhdf5 parallel DropletUtils doParallel iterators foreach Seurat ggstar: grid utils ggplot2 scales gridExtra cli sets: graphics grDevices stats utils Nebulosa: ggplot2 patchwork Seurat SingleCellExperiment SummarizedExperiment ks Matrix stats methods tenXplore: shiny restfulSE methods ontoProc SummarizedExperiment AnnotationDbi matrixStats org.Mm.eg.db stats utils AUCell: DelayedArray DelayedMatrixStats data.table graphics grDevices GSEABase Matrix methods mixtools R.utils shiny stats SummarizedExperiment BiocGenerics utils MSstatsTMT: limma lme4 lmerTest methods data.table stats utils ggplot2 grDevices graphics MSstats MSstatsConvert checkmate 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 pd.hugene.1.0.st.v1: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors benchmarkme: benchmarkmeData compiler doParallel dplyr foreach graphics httr Matrix methods parallel stringr tibble utils harmony: Rcpp dplyr cowplot ggplot2 Matrix methods tibble rlang RhpcBLASctl RcppArmadillo RcppProgress RnBeads.hg19: GenomicRanges smurf: catdata glmnet graphics MASS Matrix methods mgcv parallel RColorBrewer Rcpp stats RcppArmadillo UpSetR: ggplot2 gridExtra plyr utils stats methods grDevices scales Icens: survival graphics rvest: glue cli httr lifecycle magrittr rlang selectr tibble xml2 withr tensorflow: config processx reticulate tfruns utils yaml grDevices tfautograph rstudioapi lifecycle VGAM: methods stats stats4 splines SCnorm: SingleCellExperiment SummarizedExperiment stats methods graphics grDevices parallel quantreg cluster moments data.table BiocParallel S4Vectors ggplot2 forcats BiocGenerics getDEE2: stats utils SummarizedExperiment htm2txt NetRep: methods foreach Rcpp statmod RhpcBLASctl abind RColorBrewer utils stats graphics grDevices BH RcppArmadillo breastCancerUPP: parmigene: RProtoBufLib: MethylMix: foreach RPMM RColorBrewer ggplot2 RCurl impute data.table limma R.matlab digest mpra: methods BiocGenerics SummarizedExperiment limma S4Vectors scales stats graphics statmod mosaics: methods graphics Rcpp MASS splines lattice IRanges GenomicRanges GenomicAlignments Rsamtools GenomeInfoDb S4Vectors lsa: SnowballC TRONCO: bnlearn Rgraphviz gtools parallel foreach doParallel iterators RColorBrewer circlize igraph grid gridExtra xtable gtable scales R.matlab grDevices graphics stats utils methods DNAshapeR: GenomicRanges Rcpp Biostrings fields oligoClasses: BiocGenerics Biobase methods graphics IRanges GenomicRanges SummarizedExperiment Biostrings affyio foreach BiocManager utils S4Vectors RSQLite DBI ff coMET: grid utils biomaRt Gviz psych hash grDevices gridExtra rtracklayer IRanges S4Vectors GenomicRanges stats corrplot scReClassify: randomForest e1071 stats SummarizedExperiment SingleCellExperiment methods nnTensor: methods MASS fields rTensor plot3D tagcloud ggplot2 signatureSearch: Rcpp SummarizedExperiment org.Hs.eg.db 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 timeDate: graphics utils stats methods MSstatsSampleSize: ggplot2 BiocParallel caret gridExtra reshape2 stats utils grDevices graphics MSstats magick: Rcpp magrittr curl RNeXML: ape methods XML plyr reshape2 httr uuid dplyr tidyr stringr stringi xml2 rlang survMisc: survival graphics grDevices stats utils knitr KMsurv ggplot2 data.table zoo grid gridExtra km.ci xtable Anaquin: ggplot2 ROCR knitr qvalue locfit methods stats utils plyr DESeq2 mco: ROC: utils methods knitr IntOMICS: bnlearn bnstruct matrixStats RColorBrewer bestNormalize igraph gplots stats utils graphics numbers SummarizedExperiment ggplot2 ggraph methods cowplot grid rlang lsr: graphics grDevices methods stats RefManageR: xml2 jsonlite utils plyr tools httr lubridate stringr methods bibtex TxDb.Athaliana.BioMart.plantsmart22: GenomicFeatures AnnotationDbi messina: survival methods Rcpp plyr ggplot2 grid foreach graphics octad.db: ExperimentHub ROI: methods registry slam utils checkmate common: utils TxDb.Athaliana.BioMart.plantsmart28: GenomicFeatures AnnotationDbi prebsdata: switchde: SingleCellExperiment SummarizedExperiment dplyr ggplot2 methods stats NPARC: dplyr tidyr BiocParallel broom MASS rlang magrittr stats methods evobiR: seqinr ape geiger shiny phytools kriging: RedisParam: BiocParallel methods redux withr futile.logger tRanslatome: methods limma anota DESeq2 edgeR RankProd topGO org.Hs.eg.db GOSemSim Heatplus gplots plotrix Biobase MEEBOdata: RPA: affy BiocGenerics BiocStyle methods rmarkdown phyloseq TPP2D: stats utils dplyr methods ggplot2 tidyr foreach doParallel openxlsx stringr RCurl parallel MASS BiocParallel limma esATAC: Rsamtools GenomicRanges ShortRead pipeFrame Rcpp methods knitr Rbowtie2 rtracklayer ggplot2 Biostrings ChIPseeker clusterProfiler igraph rJava magrittr digest BSgenome AnnotationDbi GenomicAlignments GenomicFeatures R.utils GenomeInfoDb BiocGenerics S4Vectors IRanges rmarkdown tools VennDiagram grid JASPAR2018 TFBSTools grDevices graphics stats utils parallel corrplot BiocManager motifmatchr OmicsLonDA: SummarizedExperiment gss plyr zoo pracma ggplot2 BiocParallel parallel grDevices graphics stats utils methods BiocGenerics mdp: ggplot2 gridExtra grid stats utils sysfonts: breakaway: ggplot2 graphics lme4 magrittr MASS phyloseq stats tibble utils iSEEu: iSEE iSEEhex methods S4Vectors IRanges shiny SummarizedExperiment SingleCellExperiment ggplot2 DT stats colourpicker shinyAce survivalAnalysis: grDevices graphics stats utils survival rlang dplyr forcats magrittr purrr stringr tibble tidyr gridExtra ggplot2 scales survminer cowplot tidytidbits phytools: ape maps clusterGeneration coda combinat doParallel expm foreach graphics grDevices MASS methods mnormt nlme numDeriv optimParallel parallel phangorn plotrix scatterplot3d stats utils CNVgears: data.table ggplot2 MANOR: GLAD graphics grDevices stats utils GEOexplorer: shiny limma Biobase plotly shinyBS DT htmltools factoextra heatmaply maptools pheatmap scales shinyHeatmaply shinybusy ggplot2 stringr umap GEOquery impute grDevices stats graphics utils ggalluvial: ggplot2 stats dplyr tidyr lazyeval rlang tidyselect SemDist: AnnotationDbi GO.db annotate cydar: SingleCellExperiment viridis methods shiny graphics stats grDevices utils BiocGenerics S4Vectors BiocParallel SummarizedExperiment flowCore Biobase Rcpp BiocNeighbors SpatialDecon: grDevices stats utils graphics SeuratObject Biobase GeomxTools repmis methods Matrix logNormReg ASGSCA: Matrix MASS omicsPrint: MASS methods matrixStats graphics stats SummarizedExperiment MultiAssayExperiment RaggedExperiment BPRMeth: GenomicRanges assertthat methods MASS doParallel parallel e1071 earth foreach randomForest stats IRanges S4Vectors data.table graphics truncnorm mvtnorm Rcpp matrixcalc magrittr kernlab ggplot2 cowplot BiocStyle RcppArmadillo pwrEWAS.data: ExperimentHub rhdf5client: methods DelayedArray httr rjson utils data.table gwascat: methods S4Vectors IRanges GenomeInfoDb GenomicRanges GenomicFeatures readr Biostrings AnnotationDbi BiocFileCache snpStats VariantAnnotation AnnotationHub PoDCall: ggplot2 gridExtra mclust diptest rlist shiny DT LaplacesDemon purrr shinyjs readr grDevices stats utils synaptome.data: AnnotationHub rdist: Rcpp methods RcppArmadillo apcluster: Rcpp methods Matrix stats graphics grDevices mfa: methods stats ggplot2 Rcpp dplyr ggmcmc MCMCpack MCMCglmm coda magrittr tibble Biobase kableExtra: knitr magrittr stringr xml2 rvest rmarkdown scales viridisLite stats grDevices htmltools rstudioapi glue tools webshot digest graphics svglite shinyjs: digest jsonlite shiny EBSeqHMM: EBSeq dagLogo: methods grid pheatmap Biostrings UniProt.ws BiocGenerics utils biomaRt motifStack httr scBubbletree: reshape2 future future.apply ape scales Seurat ggplot2 ggtree patchwork proxy methods stats base utils pd.hg.u95a: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors OVESEG: stats utils methods BiocParallel SummarizedExperiment limma fdrtool Rcpp HilbertCurve: grid methods utils HilbertVis png grDevices circlize IRanges GenomicRanges polylabelr paircompviz: Rgraphviz GSBenchMark: marray: limma methods SWATH2stats: data.table reshape2 ggplot2 stats grDevices graphics utils biomaRt methods yamss: methods BiocGenerics SummarizedExperiment IRanges stats S4Vectors EBImage Matrix mzR data.table grDevices limma GateFinder: splancs mvoutlier methods stats diptest flowCore flowFP SC3: graphics stats utils methods e1071 parallel foreach doParallel doRNG shiny ggplot2 pheatmap ROCR robustbase rrcov cluster WriteXLS Rcpp SummarizedExperiment SingleCellExperiment BiocGenerics S4Vectors RcppArmadillo bdsmatrix: methods codetools: breastCancerVDX: CGHregions: methods Biobase CGHbase gdsfmt: methods SIMLR: parallel Matrix stats methods Rcpp pracma RcppAnnoy RSpectra rlist: yaml jsonlite XML data.table MEIGOR: Rsolnp snowfall CNORode deSolve iPAC: gdata scatterplot3d Biostrings multtest MetCirc: amap circlize scales shiny Spectra ggplot2 MsCoreUtils S4Vectors shinytest2: testthat R6 callr checkmate chromote crayon ellipsis fs globals httr jsonlite pingr rlang rmarkdown shiny withr cpp11 Uniquorn: stringr R.utils WriteXLS stats doParallel foreach GenomicRanges IRanges VariantAnnotation data.table tscR: dplyr 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limma MASS moments outliers parallel plotrix raster readbitmap reshape2 SamSPECTRAL waveslim wavethresh zoo startupmsg: PSEA: Biobase MASS KOdata: dcanr: igraph foreach plyr stringr reshape2 methods Matrix graphics stats RColorBrewer circlize doRNG illuminaHumanv1.db: methods AnnotationDbi org.Hs.eg.db listenv: Affyhgu133Plus2Expr: sigsquared: methods Biobase survival permute: stats scmap: Biobase SingleCellExperiment SummarizedExperiment BiocGenerics S4Vectors dplyr reshape2 matrixStats proxy utils googleVis ggplot2 methods stats e1071 randomForest Rcpp RcppArmadillo ggvis: assertthat jsonlite shiny magrittr dplyr rlang htmltools methods pROC: methods plyr Rcpp progeny: Biobase stats dplyr tidyr ggplot2 ggrepel gridExtra decoupleR reshape2 methylGSA: RobustRankAggreg ggplot2 stringr stats clusterProfiler missMethyl org.Hs.eg.db reactome.db BiocParallel GO.db AnnotationDbi shiny IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylationEPICanno.ilm10b4.hg19 cvAUC: ROCR data.table NanoStringQCPro: methods AnnotationDbi org.Hs.eg.db Biobase knitr NMF RColorBrewer png HDTD: stats Rcpp RcppArmadillo BADER: naniar: dplyr ggplot2 purrr tidyr tibble norm magrittr stats visdat rlang forcats viridis glue UpSetR cli vctrs assertive.data: assertive.base assertive.strings filelock: RApiSerialize: flowPlots: methods reader: utils NCmisc grDevices graphics stats methods PECA: ROTS limma affy genefilter preprocessCore aroma.affymetrix aroma.core triebeard: Rcpp rSpectral: Rcpp Rdpack igraph graph RcppArmadillo lfda: plyr grDevices rARPACK clustree: ggraph checkmate igraph dplyr grid ggplot2 viridis methods rlang tidygraph ggrepel SLqPCR: stats binr: QuasR: parallel GenomicRanges Rbowtie methods grDevices graphics utils stats tools BiocGenerics S4Vectors IRanges Biobase Biostrings BSgenome Rsamtools GenomicFeatures ShortRead BiocParallel GenomeInfoDb rtracklayer GenomicFiles AnnotationDbi Rhtslib anocva: cluster spatstat.random: spatstat.data spatstat.geom stats utils methods grDevices spatstat.utils RNAinteract: RColorBrewer ICS ICSNP cellHTS2 geneplotter gplots grid hwriter lattice latticeExtra limma methods splots abind locfit Biobase sitePath: RColorBrewer Rcpp ape aplot ggplot2 ggrepel ggtree graphics grDevices gridExtra methods parallel seqinr stats tidytree utils deconstructSigs: reshape2 BSgenome BSgenome.Hsapiens.UCSC.hg19 GenomeInfoDb grDevices graphics utils cancerclass: Biobase binom methods stats erma: methods Homo.sapiens GenomicFiles rtracklayer S4Vectors BiocGenerics GenomicRanges SummarizedExperiment ggplot2 GenomeInfoDb Biobase shiny BiocParallel IRanges AnnotationDbi rbenchmark: mygene: GenomicFeatures httr jsonlite S4Vectors Hmisc sqldf plyr sampleClassifierData: SummarizedExperiment TFMPvalue: Rcpp qqconf: MASS robustbase Rcpp proj4: nnlasso: cicero: monocle Gviz assertthat Biobase BiocGenerics data.table dplyr FNN GenomicRanges ggplot2 glasso grDevices igraph IRanges Matrix methods parallel plyr reshape2 S4Vectors stats stringi stringr tibble tidyr VGAM utils Risa: Biobase methods Rcpp biocViews affy xcms miRcompData: utils genomewidesnp6Crlmm: utils alabaster.schemas: SANTA: igraph graphics Matrix methods stats e1071: graphics grDevices class stats methods utils proxy xlsx: rJava xlsxjars grDevices utils rainbow: MASS pcaPP hdrcde cluster colorspace ks methods ppcseq: benchmarkme dplyr edgeR foreach ggplot2 graphics lifecycle magrittr methods parallel purrr Rcpp RcppParallel rlang rstan rstantools stats tibble tidybayes tidyr utils BH RcppEigen StanHeaders diffobj: crayon tools methods utils stats reshape2: plyr Rcpp stringr wavethresh: MASS distrEx: methods distr startupmsg utils stats agilp: multicrispr: assertive BiocGenerics Biostrings BSgenome CRISPRseek data.table GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 grid karyoploteR magrittr methods parallel plyranges Rbowtie reticulate rtracklayer stats stringi tidyr tidyselect utils VarfromPDB: XML XML2R curl stringr stringi RISmed utils epivizr: methods epivizrServer epivizrData GenomicRanges S4Vectors IRanges bumphunter GenomeInfoDb contrast: nlme sandwich rms BDMMAcorrect: vegan ellipse ggplot2 ape SummarizedExperiment Rcpp RcppArmadillo RcppEigen stats RMTstat: networkD3: htmlwidgets igraph magrittr sSNAPPY: ggplot2 dplyr magrittr rlang stats graphite tibble ggraph igraph reshape2 org.Hs.eg.db SummarizedExperiment edgeR methods ggforce pheatmap utils stringr gtools tidyr BRGenomics: rtracklayer GenomeInfoDb S4Vectors GenomicRanges parallel IRanges stats Rsamtools GenomicAlignments DESeq2 SummarizedExperiment utils methods annaffy: methods Biobase BiocManager GO.db AnnotationDbi DBI S4Arrays: methods Matrix abind BiocGenerics S4Vectors IRanges stats crayon BiocHubsShiny: shiny AnnotationHub ExperimentHub DT htmlwidgets S4Vectors shinyAce shinyjs shinythemes shinytoastr utils EDASeq: Biobase ShortRead methods graphics BiocGenerics IRanges aroma.light Rsamtools biomaRt Biostrings AnnotationDbi GenomicFeatures GenomicRanges BiocManager levi: DT RColorBrewer colorspace dplyr ggplot2 httr igraph reshape2 shiny shinydashboard shinyjs xml2 knitr Rcpp grid grDevices stats utils testthat methods rmarkdown ECOSolveR: methods epivizrChart: epivizrData epivizrServer htmltools rjson methods BiocGenerics patchwork: ggplot2 gtable grid stats grDevices utils graphics rlang cli slingshot: princurve stats TrajectoryUtils graphics grDevices igraph matrixStats methods S4Vectors SingleCellExperiment SummarizedExperiment mhsmm: mvtnorm methods apeglm: emdbook SummarizedExperiment GenomicRanges methods stats utils Rcpp RcppEigen RcppNumerical GenomicTuples: GenomicRanges GenomeInfoDb S4Vectors methods BiocGenerics Rcpp IRanges data.table stats4 stats utils rprojroot: TIN: data.table impute aroma.affymetrix WGCNA squash stringr fobitools: clisymbols crayon dplyr fgsea ggplot2 ggraph magrittr ontologyIndex purrr RecordLinkage stringr textclean tictoc tidygraph tidyr vroom MethylAidData: MethylAid SwathXtend: e1071 openxlsx VennDiagram lattice ClueR: e1071 parallel SynExtend: DECIPHER methods Biostrings S4Vectors IRanges utils stats parallel graphics grDevices CellBarcode: methods stats Rcpp data.table plyr ggplot2 stringr magrittr ShortRead Biostrings egg Ckmeans.1d.dp utils S4Vectors seqinr zlibbioc BH docopt: methods dendsort: CHETAH: ggplot2 SingleCellExperiment shiny plotly pheatmap bioDist dendextend cowplot corrplot grDevices stats graphics reshape2 S4Vectors SummarizedExperiment NetActivityData: ACME: Biobase methods BiocGenerics graphics stats spdep: methods spData sf stats deldir boot graphics utils grDevices units s2 e1071 sp Rmpfr: gmp stats utils methods maskBAD: gcrma affy testthat: brio callr cli desc digest ellipsis evaluate jsonlite lifecycle magrittr methods pkgload praise processx ps R6 rlang utils waldo withr GenomAutomorphism: Biostrings BiocGenerics BiocParallel GenomeInfoDb GenomicRanges IRanges dplyr data.table parallel doParallel foreach methods S4Vectors stats numbers utils admisc: methods lobstr: crayon methods prettyunits rlang cpp11 cowplot: ggplot2 grid gtable grDevices methods rlang scales sftime: sf methods epistasisGA: BiocParallel data.table matrixStats stats survival igraph batchtools qgraph grDevices parallel ggplot2 grid bigmemory graphics utils Rcpp RcppArmadillo BH WGCNA: dynamicTreeCut fastcluster stats grDevices utils matrixStats Hmisc impute splines foreach doParallel preprocessCore survival parallel GO.db AnnotationDbi Rcpp Matching: MASS graphics grDevices 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 aCGH: cluster survival multtest Biobase grDevices graphics methods stats splines utils RareVariantVis: BiocGenerics VariantAnnotation googleVis GenomicFeatures S4Vectors IRanges GenomeInfoDb GenomicRanges gtools BSgenome BSgenome.Hsapiens.UCSC.hg19 TxDb.Hsapiens.UCSC.hg19.knownGene phastCons100way.UCSC.hg19 SummarizedExperiment GenomicScores Cubist: lattice reshape2 utils Homo.sapiens: AnnotationDbi methods OrganismDbi GenomicFeatures GO.db org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene arsenal: stats knitr utils rphylopic: ggplot2 jsonlite grid graphics png grImport2 rsvg httr curl methods lifecycle pbapply knitr scRNAseqApp: bibtex bslib circlize ComplexHeatmap data.table DT GenomicRanges GenomeInfoDb ggdendro ggforce ggplot2 ggrepel ggridges grDevices grid gridExtra hdf5r htmltools IRanges jsonlite magrittr methods patchwork plotly RColorBrewer RefManageR Rsamtools rtracklayer S4Vectors scales scrypt Seurat SeuratObject shiny shinyhelper shinymanager slingshot SingleCellExperiment stats tools xfun xml2 utils tcltk: utils maxLik: miscTools methods sandwich generics VegaMC: biomaRt Biobase methods RANN: UCell: methods data.table Matrix stats BiocParallel BiocNeighbors SingleCellExperiment SummarizedExperiment vbmp: viper: Biobase methods mixtools stats parallel e1071 KernSmooth artMS: 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 DMRcate: ExperimentHub bsseq GenomeInfoDb limma edgeR DSS minfi missMethyl GenomicRanges plyr Gviz IRanges stats utils S4Vectors methods graphics SummarizedExperiment biomaRt dittoSeq: ggplot2 methods colorspace gridExtra cowplot reshape2 pheatmap grDevices ggrepel ggridges stats utils SummarizedExperiment SingleCellExperiment S4Vectors emojifont: ggplot2 proto showtext sysfonts utils plyr: Rcpp microbiomeDataSets: SummarizedExperiment TreeSummarizedExperiment MultiAssayExperiment methods utils BiocGenerics ExperimentHub Biostrings ape ribor: dplyr ggplot2 hash methods rhdf5 rlang stats S4Vectors tidyr tools yaml pcaPP: mvtnorm methods quanteda: methods fastmatch 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GenomicAlignments BiocIO tools restfulr optimParallel: stats parallel downloadthis: fs readr writexl bsplus mime htmltools magrittr zip ggplot2 base64enc phenopath: Rcpp SummarizedExperiment methods stats dplyr tibble ggplot2 tidyr gfonts: utils htmltools shiny crul jsonlite glue crayon SBMLR: XML deSolve OCplus: multtest graphics grDevices stats interp GenomicFiles: methods BiocGenerics MatrixGenerics GenomicRanges SummarizedExperiment BiocParallel Rsamtools rtracklayer GenomicAlignments IRanges S4Vectors VariantAnnotation GenomeInfoDb confintr: boot stats MOFA2: rhdf5 dplyr tidyr reshape2 pheatmap ggplot2 methods RColorBrewer cowplot ggrepel reticulate HDF5Array grDevices stats magrittr forcats utils corrplot DelayedArray Rtsne uwot basilisk stringi alabaster: alabaster.base alabaster.matrix alabaster.ranges alabaster.se alabaster.sce alabaster.spatial alabaster.string alabaster.vcf alabaster.bumpy alabaster.mae DiffLogo: stats cba grDevices graphics utils tools dcGSA: Matrix BiocParallel GenomicInteractionNodes: stats AnnotationDbi graph GO.db GenomicRanges GenomicFeatures GenomeInfoDb methods IRanges RBGL S4Vectors MetaboSignal: KEGGgraph hpar igraph RCurl KEGGREST EnsDb.Hsapiens.v75 stats graphics utils org.Hs.eg.db biomaRt AnnotationDbi MWASTools mygene gaga: Biobase coda EBarrays mgcv RGSEA: BiocGenerics backports: RgnTX: GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 graphics IRanges methods regioneR S4Vectors stats TxDb.Hsapiens.UCSC.hg19.knownGene DMRScan: Matrix MASS RcppRoll GenomicRanges IRanges GenomeInfoDb methods mvtnorm stats parallel gage: graph KEGGREST AnnotationDbi GO.db swfdr: methods splines stats4 stats tRNAscanImport: GenomicRanges tRNA methods stringr BiocGenerics Biostrings Structstrings S4Vectors IRanges XVector GenomeInfoDb rtracklayer BSgenome Rsamtools BridgeDbR: rJava curl ROTS: Rcpp stats Biobase methods BiRewire: igraph slam Rtsne Matrix breakpointRdata: ADAM: stats utils methods Rcpp GO.db KEGGREST knitr pbapply dplyr DT stringr SummarizedExperiment BSgenome.Dmelanogaster.UCSC.dm3: BSgenome optparse: methods getopt XNAString: utils Biostrings BSgenome data.table GenomicRanges IRanges methods Rcpp stringi S4Vectors future.apply stringr formattable stats googleVis: methods jsonlite utils drtmle: SuperLearner np future.apply shinyFiles: htmltools jsonlite tools shiny fs tibble BSgenome.Dmelanogaster.UCSC.dm6: BSgenome DiagrammeR: dplyr downloader glue htmltools htmlwidgets igraph magrittr purrr RColorBrewer readr rlang rstudioapi scales stringr tibble tidyr viridis visNetwork HELP: stats graphics grDevices Biobase methods karyoploteR: regioneR GenomicRanges methods IRanges Rsamtools stats graphics memoise rtracklayer GenomeInfoDb S4Vectors biovizBase digest bezier GenomicFeatures bamsignals AnnotationDbi grDevices VariantAnnotation INTACT: SQUAREM bdsmatrix numDeriv stats DepecheR: ggplot2 MASS Rcpp dplyr gplots viridis foreach doSNOW matrixStats mixOmics moments grDevices graphics stats utils methods 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methods utils lpSolve: TOP: 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 sabre: dplyr entropy raster rlang sf tibble tidyr VanillaICE: BiocGenerics GenomicRanges SummarizedExperiment MatrixGenerics Biobase S4Vectors IRanges oligoClasses foreach matrixStats data.table grid lattice methods GenomeInfoDb crlmm tools stats utils BSgenome.Hsapiens.UCSC.hg18 gcapc: BiocGenerics GenomeInfoDb S4Vectors IRanges Biostrings BSgenome GenomicRanges Rsamtools GenomicAlignments matrixStats MASS splines grDevices graphics stats methods arrow: assertthat bit64 glue methods purrr R6 rlang stats tidyselect utils vctrs cpp11 biwt: robustbase MASS zeallot: rearrr: checkmate dplyr lifecycle plyr purrr rlang R6 stats tibble utils ChemoSpecUtils: data.table ggplot2 ggrepel plotly magrittr GenomicAlignments: methods BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges SummarizedExperiment Biostrings Rsamtools utils stats BiocParallel distr: methods graphics startupmsg sfsmisc stats grDevices utils MASS SigCheck: MLInterfaces Biobase e1071 BiocParallel survival graphics stats utils methods Rtreemix: methods graph Biobase Hmisc rootSolve: stats graphics grDevices cachem: rlang fastmap mdqc: cluster MASS FME: deSolve rootSolve coda minpack.lm MASS graphics grDevices stats utils minqa tippy: htmlwidgets htmltools shiny jsonlite CCPROMISE: stats methods CCP PROMISE Biobase GSEABase utils fauxpas: R6 httpcode whisker rjags: coda TPP: Biobase dplyr magrittr tidyr biobroom broom data.table doParallel foreach futile.logger ggplot2 grDevices gridExtra grid knitr limma MASS mefa nls2 openxlsx parallel plyr purrr RColorBrewer RCurl reshape2 rmarkdown splines stats stringr tibble utils VennDiagram VGAM checkmate: backports utils rARPACK: RSpectra QFeatures: MultiAssayExperiment methods stats utils S4Vectors IRanges SummarizedExperiment BiocGenerics ProtGenerics AnnotationFilter lazyeval Biobase MsCoreUtils igraph plotly MSnbase: methods BiocGenerics Biobase mzR S4Vectors ProtGenerics MsCoreUtils BiocParallel IRanges plyr vsn grid stats4 affy impute pcaMethods MALDIquant mzID digest lattice ggplot2 XML scales MASS Rcpp miRNAtap.db: miRNAtap AnnotationDbi DBI RSQLite clock: cli lifecycle rlang tzdb vctrs cpp11 GA4GHclient: S4Vectors BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges httr IRanges jsonlite methods VariantAnnotation RDRToolbox: graphics grDevices methods stats MASS rgl flowWorkspace: Biobase BiocGenerics cytolib XML ggplot2 graph graphics grDevices methods stats stats4 utils RBGL tools Rgraphviz data.table dplyr scales matrixStats RProtoBufLib flowCore ncdfFlow DelayedArray S4Vectors cpp11 BH Rhdf5lib TNBC.CMS: e1071 quadprog SummarizedExperiment GSVA pheatmap grDevices RColorBrewer pracma GGally R.utils forestplot ggplot2 ggpubr survival grid stats methods CGHnormaliter: 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annotate org.Hs.eg.db AnnotationDbi topGO cluster flexmix RBGL graph Matrix corpcor Rcpp pkgDepTools: methods graph RBGL vcfR: ape dplyr graphics grDevices magrittr memuse methods pinfsc50 Rcpp stats stringr tibble utils vegan viridisLite ALLMLL: affy RadioGx: CoreGx SummarizedExperiment BiocGenerics data.table S4Vectors Biobase parallel BiocParallel RColorBrewer caTools magicaxis methods reshape2 scales grDevices graphics stats utils assertthat matrixStats downloader radiant.data: magrittr ggplot2 lubridate tidyr dplyr tibble rlang arrow broom car knitr markdown rmarkdown shiny jsonlite shinyAce psych DT readr readxl writexl scales curl rstudioapi import plotly glue shinyFiles stringi randomizr patchwork bslib png MASS base64enc cubature: Rcpp NADfinder: BiocGenerics IRanges GenomicRanges S4Vectors SummarizedExperiment graphics methods baseline signal GenomicAlignments GenomeInfoDb rtracklayer limma trackViewer stats utils Rsamtools metap EmpiricalBrownsMethod ATACseqQC corrplot csaw 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tools shiny BoolNet: igraph XML Cormotif: affy limma graphics grDevices randtests: TeachingDemos: rematch: ReadqPCR: Biobase methods nsga2R: mco consICA: fastICA sm org.Hs.eg.db GO.db stats SummarizedExperiment BiocParallel graph methods pheatmap survival topGO graphics grDevices brew: FCBF: ggplot2 gridExtra pbapply parallel SummarizedExperiment stats mclust SPOTlight: ggplot2 NMF Matrix matrixStats nnls SingleCellExperiment stats mlr3: R6 backports checkmate data.table evaluate future future.apply lgr mlbench mlr3measures mlr3misc parallelly palmerpenguins paradox uuid flagme: gcspikelite xcms CAMERA gplots graphics MASS methods SparseM stats utils RcppProgress: puma: oligo graphics grDevices methods stats utils mclust oligoClasses Biobase affy affyio verification: methods fields boot CircStats MASS dtw graphics stats vsn: methods Biobase affy limma lattice ggplot2 HTqPCR: Biobase RColorBrewer limma affy gplots graphics grDevices methods stats stats4 utils PWMEnrich: methods BiocGenerics Biostrings grid seqLogo gdata evd S4Vectors protViz: methods Rcpp HiTC: methods IRanges GenomicRanges Biostrings graphics grDevices rtracklayer RColorBrewer Matrix parallel GenomeInfoDb sass: fs rlang htmltools R6 rappdirs ssPATHS: SummarizedExperiment ROCR dml MESS chemometrics: rpart class e1071 MASS nnet pcaPP robustbase som lars pls mclust gridBase: graphics grid BiocFileCache: dbplyr methods stats utils dplyr RSQLite DBI filelock curl httr rjsoncons: jsonlite cpp11 IgGeneUsage: methods reshape2 Rcpp RcppParallel rstan rstantools SummarizedExperiment BH RcppEigen StanHeaders rappdirs: QUBIC: biclust Rcpp methods Matrix RcppArmadillo Rcwl: yaml methods S4Vectors utils stats BiocParallel batchtools DiagrammeR shiny R.utils codetools basilisk ARRmData: PMCMRplus: mvtnorm multcompView gmp Rmpfr SuppDists kSamples BWStest MASS stats AnVILWorkflow: utils AnVIL httr methods jsonlite datawizard: insight stats utils RepViz: GenomicRanges Rsamtools IRanges biomaRt S4Vectors graphics grDevices utils biocViews: Biobase graph methods RBGL tools utils XML RCurl RUnit BiocManager farver: NLP: utils intergraph: network igraph utils savR: ggplot2 methods reshape2 scales gridExtra XML benchmarkmeData: dplyr graphics tibble utils qsvaR: SummarizedExperiment sva stats ggplot2 methods vctrs: cli glue lifecycle rlang TileDBArray: DelayedArray methods Rcpp tiledb S4Vectors R453Plus1Toolbox: methods VariantAnnotation Biostrings Biobase utils grDevices graphics stats tools xtable R2HTML TeachingDemos BiocGenerics S4Vectors IRanges XVector GenomicRanges SummarizedExperiment biomaRt BSgenome Rsamtools ShortRead NMF: methods utils registry rngtools cluster graphics stats stringr digest grid grDevices gridBase colorspace RColorBrewer foreach doParallel ggplot2 reshape2 Biobase codetools BiocManager selectr: methods stringr R6 elsa: methods sp raster NMI: topGO: methods BiocGenerics graph Biobase GO.db AnnotationDbi SparseM lattice matrixStats DBI runonce: bigassertr urltools rae230aprobe: AnnotationDbi TxDb.Mmusculus.UCSC.mm10.knownGene: GenomicFeatures AnnotationDbi ibh: simpIntLists methylscaper: shiny shinyjs seriation BiocParallel seqinr Biostrings Rfast grDevices graphics stats utils tools methods shinyFiles data.table SummarizedExperiment multtest: methods BiocGenerics Biobase survival MASS stats4 cplm: coda Matrix splines methods biglm ggplot2 minqa nlme reshape2 statmod stats stats4 tweedie R4RNA: Biostrings splots: grid RColorBrewer RNAsense: ggplot2 parallel NBPSeq qvalue SummarizedExperiment stats utils methods DrugVsDiseasedata: RTCGA.clinical: RTCGA textshape: data.table slam stats stringi utils ica: colorBlindness: ggplot2 grDevices methods cowplot colorspace graphics gridGraphics gtable grid sparrow: babelgene BiocGenerics BiocParallel BiocSet checkmate circlize ComplexHeatmap data.table DelayedMatrixStats edgeR ggplot2 graphics grDevices GSEABase irlba limma Matrix methods plotly stats utils viridis aggregateBioVar: stats methods S4Vectors SummarizedExperiment SingleCellExperiment Matrix tibble rlang timescape: htmlwidgets jsonlite stringr dplyr gtools brio: condiments: slingshot mgcv RANN stats SingleCellExperiment SummarizedExperiment utils magrittr dplyr Ecume methods pbapply matrixStats BiocParallel TrajectoryUtils igraph distinct bitops: httptest: testthat curl digest httr jsonlite stats utils scMET: methods Rcpp RcppParallel rstan rstantools VGAM data.table MASS logitnorm ggplot2 matrixStats assertthat viridis coda BiocStyle cowplot stats SummarizedExperiment SingleCellExperiment Matrix dplyr S4Vectors BH RcppEigen StanHeaders ggnetwork: ggplot2 ggrepel network igraph sna utils stats4: graphics methods stats assertive.models: assertive.base stats GenSA: CellaRepertorium: dplyr tibble stringr Biostrings Rcpp reshape2 methods rlang purrr Matrix S4Vectors BiocGenerics tidyr forcats progress stats utils generics glue meshr: markdown rmarkdown BiocStyle knitr methods stats utils fdrtool MeSHDbi Category S4Vectors BiocGenerics RSQLite qsmooth: SummarizedExperiment utils sva stats methods graphics Hmisc bigmemory: bigmemory.sri methods utils Rcpp uuid BH HiCDCPlus: Rcpp InteractionSet GenomicInteractions bbmle pscl BSgenome data.table dplyr tidyr GenomeInfoDb rlang splines MASS GenomicRanges IRanges tibble R.utils Biostrings rtracklayer methods S4Vectors MEAL: Biobase MultiDataSet GenomicRanges limma vegan BiocGenerics minfi IRanges S4Vectors methods parallel ggplot2 permute Gviz missMethyl isva SummarizedExperiment SmartSVA graphics stats utils matrixStats synapter: methods MSnbase RColorBrewer lattice qvalue multtest utils tools Biobase Biostrings cleaver readr rmarkdown normalize450K: Biobase illuminaio quadprog utils isva: qvalue fastICA JADE umap: Matrix methods openssl reticulate Rcpp RSpectra stats pdInfoBuilder: methods Biobase RSQLite affxparser oligo Biostrings BiocGenerics DBI IRanges oligoClasses S4Vectors OutSplice: AnnotationDbi GenomicRanges GenomicFeatures IRanges org.Hs.eg.db Repitools TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene S4Vectors pvac: affy stats Biobase SICtools: methods Rsamtools doParallel Biostrings stringr matrixStats plyr GenomicRanges IRanges ChIC.data: genomeIntervals randomForest caret npGSEA: GSEABase Biobase methods BiocGenerics graphics stats MEAT: impute dynamicTreeCut glmnet grDevices graphics stats utils stringr tibble RPMM minfi dplyr SummarizedExperiment wateRmelon SparseSignatures: NMF nnlasso nnls parallel data.table Biostrings GenomicRanges IRanges BSgenome GenomeInfoDb ggplot2 gridExtra reshape2 GeneOverlap: stats RColorBrewer gplots methods hgu133acdf: utils AnnotationDbi kissDE: aods3 Biobase DESeq2 DSS ggplot2 gplots graphics grDevices matrixStats stats utils foreach doParallel parallel shiny shinycssloaders ade4 factoextra DT idr: stats ids: openssl uuid contiBAIT: BH Rsamtools data.table grDevices clue cluster gplots BiocGenerics S4Vectors IRanges GenomicRanges Rcpp TSP GenomicFiles 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GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene TxDb.Mmusculus.UCSC.mm9.knownGene org.Hs.eg.db org.Mm.eg.db rGREAT pheatmap ggplot2 EnrichedHeatmap ComplexHeatmap grid circlize BiocParallel rtracklayer GenomeInfoDb grDevices rlang tiff Rsamtools breastCancerMAINZ: BSgenome.Hsapiens.NCBI.GRCh38: BSgenome pvca: Matrix Biobase vsn stats lme4 COSNet: 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 BSgenome: methods BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges Biostrings rtracklayer utils stats matrixStats XVector Rsamtools markdown: utils commonmark xfun afex: lme4 pbkrtest lmerTest car reshape2 stats methods utils SeqSQC: ExperimentHub SNPRelate e1071 GenomicRanges gdsfmt ggplot2 GGally IRanges methods rbokeh RColorBrewer reshape2 rmarkdown S4Vectors stats utils yeastExpData: graph alabaster.bumpy: BumpyMatrix alabaster.base methods Matrix BiocGenerics S4Vectors IRanges bladderbatch: Biobase scatterHatch: grid ggplot2 plyr spatstat.geom stats grDevices lexicon: data.table syuzhet twilight: splines stats Biobase graphics grDevices REDseq: BiocGenerics BSgenome.Celegans.UCSC.ce2 multtest Biostrings BSgenome ChIPpeakAnno AnnotationDbi graphics IRanges stats utils FRGEpistasis: MASS fda methods stats utils cosmiq: Rcpp pracma xcms MassSpecWavelet faahKO seewave: graphics grDevices stats utils tuneR methods ORFik: IRanges GenomicRanges GenomicAlignments AnnotationDbi Biostrings biomaRt biomartr BiocGenerics BiocParallel BSgenome cowplot curl RCurl data.table DESeq2 dplyr downloader fst GenomeInfoDb GenomicFeatures ggplot2 gridExtra httr jsonlite methods R.utils Rcpp readr Rsamtools rtracklayer stats stringr SummarizedExperiment S4Vectors tools tibble utils XML xml2 withr easycsv: data.table jsonvalidate: V8 airway: SummarizedExperiment Pviz: Gviz biovizBase Biostrings GenomicRanges IRanges data.table methods cn.farms: Biobase methods ff oligoClasses snow DBI affxparser oligo DNAcopy preprocessCore lattice CORREP: e1071 stats futile.options: affy: BiocGenerics Biobase affyio BiocManager graphics grDevices methods preprocessCore stats utils zlibbioc MDTS: GenomicAlignments GenomicRanges IRanges Biostrings DNAcopy Rsamtools parallel stringr PanomiR: clusterProfiler dplyr forcats GSEABase igraph limma metap org.Hs.eg.db parallel preprocessCore RColorBrewer rlang tibble withr utils flowWorkspaceData: org.Pt.eg.db: methods AnnotationDbi GenomicDistributions: IRanges GenomicRanges data.table ggplot2 reshape2 methods utils Biostrings plyr dplyr scales broom GenomeInfoDb stats leiden: methods reticulate Matrix igraph doParallel: foreach iterators parallel utils R3CPET: Rcpp methods parallel ggplot2 pheatmap clValid igraph data.table reshape2 Hmisc RCurl BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges ggbio consensusSeekeR: BiocGenerics IRanges GenomicRanges BiocParallel GenomeInfoDb rtracklayer stringr S4Vectors methods seqinr: ade4 segmented restfulSEData: SummarizedExperiment ExperimentHub DelayedArray HDF5Array utils methods GraphPAC: iPAC igraph TSP RMallow RPostgres: bit64 blob DBI hms lubridate methods Rcpp withr plogr transomics2cytoscape: RCy3 KEGGREST dplyr purrr tibble SiPSiC: Matrix SingleCellExperiment signalHsmm: graphics seqinr shiny stats utils Rcpp MMAPPR2data: Rsamtools pRoloc: MSnbase MLInterfaces methods Rcpp BiocParallel stats4 Biobase mclust 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 RcppArmadillo crlmm: oligoClasses preprocessCore methods Biobase BiocGenerics affyio illuminaio ellipse mvtnorm splines stats utils lattice ff foreach RcppEigen matrixStats VGAM parallel graphics limma beanplot tomoseqr: grDevices graphics animation tibble dplyr stringr purrr methods shiny BiocFileCache readr tools plotly ggplot2 pfamAnalyzeR: readr stringr dplyr utils tibble magrittr MACSQuantifyR: readxl graphics tools utils grDevices ggplot2 ggrepel methods stats latticeExtra lattice rmarkdown png grid gridExtra prettydoc rvest xml2 RMariaDB: bit64 blob DBI hms lubridate methods rlang cpp11 plogr excluderanges: GenomicRanges leidenbase: igraph WES.1KG.WUGSC: animation: magick BiocIO: BiocGenerics S4Vectors methods tools binom: msd16s: Biobase metagenomeSeq ggrepel: ggplot2 grid Rcpp rlang scales withr TDbasedUFE: GenomicRanges rTensor readr methods MOFAdata tximport tximportData graphics stats utils shiny ddPCRclust: plotrix clue parallel ggplot2 openxlsx R.utils flowCore flowDensity SamSPECTRAL flowPeaks pushbar: shiny jsonlite fftwtools: destiny: methods graphics grDevices grid 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ggrepel methods SpotClean: stats methods utils dplyr S4Vectors SummarizedExperiment SpatialExperiment Matrix rhdf5 ggplot2 grid readbitmap rjson tibble viridis grDevices RColorBrewer Seurat rlang pbivnorm: qvalue: splines ggplot2 grid reshape2 monaLisa: methods stats utils grDevices graphics BiocGenerics GenomicRanges TFBSTools Biostrings IRanges stabs BSgenome glmnet S4Vectors SummarizedExperiment BiocParallel grid circlize ComplexHeatmap XVector GenomeInfoDb tools vioplot HilbertVis: grid lattice pkgdown: bslib callr cli desc digest downlit fs httr jsonlite magrittr memoise purrr ragg rlang rmarkdown tibble whisker withr xml2 yaml mathjaxr: GeneticsPed: MASS gdata genetics xmapbridge: methods stageR: SummarizedExperiment methods stats crochet: methods eudysbiome: plyr Rsamtools R.utils Biostrings biomaRt: methods utils XML AnnotationDbi progress stringr httr digest BiocFileCache rappdirs xml2 purrr: cli lifecycle magrittr rlang vctrs diffGeneAnalysis: graphics grDevices minpack.lm stats utils spqn: ggplot2 ggridges SummarizedExperiment BiocGenerics graphics stats utils matrixStats PathNet: sigPathway: parglms: methods BiocGenerics BatchJobs foreach doParallel ComplexHeatmap: methods grid graphics stats grDevices circlize GetoptLong colorspace clue RColorBrewer GlobalOptions png digest IRanges matrixStats foreach doParallel codetools gmoviz: circlize GenomicRanges graphics grid gridBase Rsamtools ComplexHeatmap BiocGenerics Biostrings GenomeInfoDb methods GenomicAlignments GenomicFeatures IRanges rtracklayer pracma colorspace S4Vectors miloR: edgeR BiocNeighbors BiocGenerics SingleCellExperiment Matrix S4Vectors stats stringr methods igraph irlba cowplot BiocParallel BiocSingular limma ggplot2 tibble matrixStats ggraph gtools SummarizedExperiment patchwork tidyr dplyr ggrepel ggbeeswarm RColorBrewer grDevices ACE: Biobase QDNAseq ggplot2 grid stats utils methods grDevices GenomicRanges glmmTMB: methods TMB lme4 Matrix nlme numDeriv mgcv RcppEigen apComplex: graph RBGL Rgraphviz stats org.Sc.sgd.db circlize: graphics GlobalOptions shape grDevices utils stats colorspace methods grid mvtnorm: stats matrixStats: GladiaTOX: data.table DBI RMySQL RSQLite numDeriv RColorBrewer parallel stats methods graphics grDevices xtable tools brew stringr RJSONIO ggplot2 ggrepel tidyr utils RCurl XML svGUI: iCARE: plotrix gtools Hmisc ontoProc: ontologyIndex Biobase S4Vectors methods stats utils BiocFileCache shiny graph Rgraphviz ontologyPlot dplyr magrittr DT igraph AnnotationHub SummarizedExperiment sparsesvd: Matrix methods bibtex: backports utils 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 nnNorm: marray graphics grDevices methods nnet stats MafDb.1Kgenomes.phase1.hs37d5: GenomicScores utils S4Vectors IRanges GenomicRanges GenomeInfoDb BSgenome Ularcirc: 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parallel reshape2 scater scuttle scran stats SummarizedExperiment SingleCellExperiment shinydashboard S4Vectors spsComps tibble utils xml2 biodbChebi: R6 biodb actuar: stats graphics expint metap: lattice Rdpack TFisher mutoss mathjaxr qqconf pathview: KEGGgraph XML Rgraphviz graph png AnnotationDbi org.Hs.eg.db KEGGREST methods utils energy: Rcpp stats boot gsl CNVPanelizer: GenomicRanges BiocGenerics S4Vectors grDevices stats utils NOISeq IRanges Rsamtools exomeCopy foreach ggplot2 plyr GenomeInfoDb gplots reshape2 stringr testthat graphics methods shiny shinyFiles shinyjs grid openxlsx targetscan.Hs.eg.db: methods AnnotationDbi trigger: corpcor qtl qvalue methods graphics sva scviR: basilisk shiny SingleCellExperiment reticulate BiocFileCache utils pheatmap SummarizedExperiment S4Vectors limma scater RTCGA.rnaseq: RTCGA lmerTest: lme4 stats methods numDeriv MASS ggplot2 GARS: ggplot2 cluster DaMiRseq MLSeq stats methods SummarizedExperiment CVXR: methods R6 Matrix Rcpp bit64 gmp Rmpfr ECOSolveR scs stats osqp RcppEigen wpm: utils methods cli Biobase SummarizedExperiment config golem shiny DT ggplot2 dplyr rlang stringr shinydashboard shinyWidgets shinycustomloader RColorBrewer logging openssl: askpass Modstrings: Biostrings methods BiocGenerics GenomicRanges S4Vectors IRanges XVector stringi stringr crayon grDevices mitoClone2: reshape2 GenomicRanges pheatmap deepSNV grDevices graphics stats utils S4Vectors Rhtslib parallel methods ggplot2 biodb: BiocFileCache R6 RCurl RSQLite Rcpp XML chk git2r jsonlite lgr lifecycle methods openssl plyr progress rappdirs stats stringr tools withr yaml testthat PWMEnrich.Hsapiens.background: methods PWMEnrich iml: checkmate data.table Formula future future.apply ggplot2 Metrics prediction R6 cobalt: stats utils grid grDevices ggplot2 gtable gridExtra chk rlang crayon backports ChIPexoQualExample: NanoTube: Biobase ggplot2 limma fgsea methods reshape stats utils MicrobiomeProfiler: clusterProfiler config DT enrichplot golem gson methods magrittr shiny shinyWidgets shinycustomloader htmltools ggplot2 graphics stats utils biodbUniprot: R6 biodb gcatest: methods lfa MBASED: RUnit BiocGenerics BiocParallel GenomicRanges SummarizedExperiment PREDAsampledata: methods PREDA Biobase affy annotate GEOfastq: xml2 rvest stringr RCurl doParallel foreach plyr MafDb.1Kgenomes.phase3.hs37d5: GenomicScores utils S4Vectors IRanges GenomicRanges GenomeInfoDb BSgenome MsCoreUtils: methods S4Vectors MASS stats clue Rcpp BSgenome.Hsapiens.UCSC.hg19.masked: BSgenome BSgenome.Hsapiens.UCSC.hg19 SparseDC: stats segmentSeq: methods baySeq S4Vectors parallel GenomicRanges ShortRead stats Rsamtools IRanges GenomeInfoDb graphics grDevices utils abind SCLCBam: webdriver: callr base64enc curl debugme httr jsonlite R6 showimage utils withr scam: mgcv methods stats graphics Matrix splines RecordLinkage: DBI RSQLite ff e1071 rpart ada ipred stats evd methods data.table nnet xtable SparseM: methods graphics stats utils fracdiff: stats geneAttribution: utils GenomicRanges org.Hs.eg.db BiocGenerics GenomeInfoDb GenomicFeatures IRanges rtracklayer ini: RTCGA.mRNA: RTCGA GeneStructureTools: Biostrings GenomicRanges IRanges data.table plyr stringdist stringr S4Vectors BSgenome.Mmusculus.UCSC.mm10 stats utils Gviz rtracklayer methods FCPS: mclust ggplot2 DataVisualizations Sconify: tibble dplyr FNN flowCore Rtsne ggplot2 magrittr utils stats readr snpStats: survival Matrix methods graphics grDevices stats utils BiocGenerics zlibbioc reticulate: Matrix Rcpp RcppTOML graphics here jsonlite methods png rappdirs utils rlang withr ExtDist: numDeriv optimx additivityTests: schex: SingleCellExperiment Seurat ggplot2 shiny hexbin stats methods cluster dplyr entropy ggforce scales grid concaveman OmnipathR: checkmate crayon curl digest dplyr httr igraph jsonlite later logger magrittr progress purrr rappdirs readr readxl rlang rmarkdown rvest stats stringr tibble tidyr tidyselect tools utils withr xml2 yaml treekoR: stats utils 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Biobase stats biwt gtools MASS tools dplyr methods utils proBAMr: IRanges AnnotationDbi GenomicRanges Biostrings GenomicFeatures rtracklayer dupRadar: Rsubread KernSmooth colonCA: Biobase TBX20BamSubset: Rsamtools xtable multiOmicsViz: methods parallel doParallel foreach grDevices graphics utils SummarizedExperiment stats concordexR: BiocParallel cli DelayedArray ggplot2 Matrix methods pheatmap rlang scales shinyBS: shiny htmltools scDataviz: S4Vectors SingleCellExperiment ggplot2 ggrepel flowCore umap Seurat reshape2 scales RColorBrewer corrplot stats grDevices graphics utils MASS matrixStats methods AlgDesign: MSQC: graphics stats utils rgl maptree: cluster rpart aroma.affymetrix: R.utils aroma.core methods R.methodsS3 R.oo R.cache R.devices R.filesets aroma.apd MASS splines matrixStats listenv future ALDEx2: methods stats zCompositions Rfast BiocParallel GenomicRanges IRanges S4Vectors SummarizedExperiment multtest chipenrich: AnnotationDbi BiocGenerics chipenrich.data GenomeInfoDb 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grDevices survival terra: methods Rcpp BEARscc: ggplot2 SingleCellExperiment data.table stats utils graphics compiler extRemes: Lmoments distillery graphics stats methods missMDA: FactoMineR ggplot2 graphics grDevices mice mvtnorm stats utils doParallel parallel foreach diggitdata: Biobase methods viper TxDb.Hsapiens.UCSC.hg19.knownGene: GenomicFeatures AnnotationDbi scMerge: BiocParallel BiocSingular BiocNeighbors cluster DelayedArray DelayedMatrixStats distr igraph M3Drop proxyC ruv cvTools scater batchelor scran methods S4Vectors SingleCellExperiment SummarizedExperiment mclustcomp: Rcpp Rdpack RcppArmadillo clipr: utils rGenomeTracksData: AnnotationHub hyperdraw: methods grid graph hypergraph Rgraphviz stats4 RNASeqPower: progressr: digest utils lamW: Rcpp RcppParallel TreeTools: ape bit64 lifecycle colorspace fastmatch methods PlotTools RCurl R.cache Rdpack Rcpp spacetime: graphics utils stats methods lattice sp zoo xts intervals katdetectr: BiocParallel changepoint changepoint.np 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