biodbExpasy: biodb R6 stringr chk RcppAlgos: gmp methods cpp11 NeighborNet: methods graph stats xcoredata: ExperimentHub utils ggseqlogo: ggplot2 BMA: survival leaps robustbase inline rrcov methods foreach: codetools utils iterators consensusDE: BiocGenerics airway AnnotationDbi BiocParallel Biobase Biostrings data.table dendextend DESeq2 EDASeq ensembldb edgeR EnsDb.Hsapiens.v86 GenomicAlignments GenomicFeatures limma org.Hs.eg.db pcaMethods RColorBrewer Rsamtools RUVSeq S4Vectors stats SummarizedExperiment TxDb.Dmelanogaster.UCSC.dm3.ensGene utils duckdb: DBI methods utils pd.hg.u95av2: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors Rttf2pt1: scales: cli farver glue labeling lifecycle munsell R6 RColorBrewer rlang viridisLite h5vcData: vulcandata: utils ChIPQC: ggplot2 DiffBind GenomicRanges BiocParallel BiocGenerics S4Vectors IRanges Rsamtools GenomicAlignments chipseq gtools methods reshape2 Nozzle.R1 Biobase grDevices stats utils GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg18.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene TxDb.Mmusculus.UCSC.mm9.knownGene TxDb.Rnorvegicus.UCSC.rn4.ensGene TxDb.Celegans.UCSC.ce6.ensGene TxDb.Dmelanogaster.UCSC.dm3.ensGene pathRender: graph Rgraphviz RColorBrewer cMAP AnnotationDbi methods stats4 squash: graphics grDevices methods stats HPAStainR: dplyr tidyr utils stats scales stringr tibble shiny data.table flexdashboard: bslib grDevices htmltools htmlwidgets jsonlite knitr rmarkdown sass scales shiny tools utils ccmap: AnnotationDbi BiocManager ccdata doParallel data.table foreach parallel xgboost lsa philentropy: Rcpp KernSmooth poorman rngtools: methods digest utils stats parallel eulerr: GenSA graphics grDevices grid polyclip polylabelr Rcpp stats utils RcppArmadillo parallel: tools compiler ternarynet: utils igraph methods graphics stats BiocParallel genomation: grid Biostrings BSgenome data.table GenomeInfoDb GenomicRanges GenomicAlignments S4Vectors ggplot2 gridBase impute IRanges matrixStats methods parallel plotrix plyr readr reshape2 Rsamtools seqPattern rtracklayer Rcpp mnormt: objectProperties: objectSignals methods TargetScoreData: SQUAREM: ccdata: LowMACA: cBioPortalData parallel stringr reshape2 data.table RColorBrewer methods LowMACAAnnotation BiocParallel motifStack Biostrings httr grid gridBase plyr shinydashboard: utils shiny htmltools promises igvR: GenomicRanges GenomicAlignments BrowserViz methods BiocGenerics httpuv utils rtracklayer VariantAnnotation RColorBrewer httr rsparse: methods Matrix MatrixExtra Rcpp data.table float RhpcBLASctl lgr RcppArmadillo Metrics: fontBitstreamVera: DESpace: edgeR limma dplyr stats Matrix SpatialExperiment ggplot2 ggpubr scales SummarizedExperiment S4Vectors BiocGenerics data.table assertthat cowplot ggforce ggnewscale patchwork BiocParallel methods MethylSeekR: rtracklayer parallel mhsmm IRanges BSgenome GenomicRanges geneplotter graphics grDevices stats utils smoothie: relimp: stats utils struct: methods ontologyIndex datasets graphics stats utils knitr SummarizedExperiment S4Vectors rols GSgalgoR: cluster doParallel foreach matchingR nsga2R survival proxy stats methods STROMA4: Biobase BiocParallel cluster matrixStats stats graphics utils PANR: igraph graphics grDevices MASS methods pvclust stats utils RedeR BicARE: Biobase multtest GSEABase GO.db methods ramwas: methods filematrix graphics stats utils digest glmnet KernSmooth grDevices GenomicAlignments Rsamtools parallel biomaRt Biostrings BiocGenerics PROcess: Icens graphics grDevices stats utils RPostgreSQL: methods DBI Rdisop: Rcpp rmutil: phangorn: ape digest fastmatch generics graphics grDevices igraph Matrix methods parallel quadprog Rcpp stats utils BLMA: ROntoTools GSA PADOG limma graph stats utils parallel Biobase metafor methods smoother: TTR fastcluster: qgraph: Rcpp methods grDevices psych lavaan plyr Hmisc igraph jpeg png colorspace Matrix corpcor reshape2 ggplot2 glasso fdrtool gtools parallel pbapply abind goseq: BiasedUrn geneLenDataBase mgcv graphics stats utils AnnotationDbi GO.db BiocGenerics sjlabelled: insight datawizard stats tools utils covEB: mvtnorm igraph gsl Biobase stats LaplacesDemon Matrix TVTB: methods utils stats AnnotationFilter BiocGenerics BiocParallel Biostrings ensembldb ensemblVEP GenomeInfoDb GenomicRanges GGally ggplot2 Gviz limma IRanges reshape2 Rsamtools S4Vectors SummarizedExperiment VariantAnnotation TargetSearch: graphics grDevices methods ncdf4 stats utils assertthat SeqGate: S4Vectors SummarizedExperiment GenomicRanges stats methods BiocManager SPsimSeq: stats methods SingleCellExperiment fitdistrplus graphics edgeR Hmisc WGCNA limma mvtnorm phyloseq utils 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 stringr 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 synapsis: EBImage stats utils graphics csaw: GenomicRanges SummarizedExperiment Rcpp Matrix BiocGenerics Rsamtools edgeR limma methods S4Vectors IRanges GenomeInfoDb stats BiocParallel metapod utils Rhtslib zlibbioc import: 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 scDblFinder: SingleCellExperiment igraph Matrix BiocGenerics BiocParallel BiocNeighbors BiocSingular S4Vectors SummarizedExperiment scran scater scuttle bluster methods DelayedArray xgboost stats utils MASS IRanges GenomicRanges GenomeInfoDb Rsamtools rtracklayer CODEX: Rsamtools GenomeInfoDb BSgenome.Hsapiens.UCSC.hg19 IRanges Biostrings S4Vectors shinytoastr: shiny spatstat.data: spatstat.utils Matrix M3DExampleData: MouseFM: httr curl GenomicRanges dplyr ggplot2 reshape2 scales gtools tidyr data.table jsonlite rlist GenomeInfoDb methods biomaRt stats IRanges org.Sc.sgd.db: methods AnnotationDbi MethTargetedNGS: stringr seqinr gplots Biostrings aroma.apd: R.methodsS3 R.oo R.utils R.huge tRNAdbImport: GenomicRanges Modstrings Structstrings tRNA Biostrings stringr httr2 xml2 S4Vectors methods IRanges utils HGNChelper: methods utils praznik: GOexpress: grid stats graphics Biobase biomaRt stringr ggplot2 RColorBrewer gplots randomForest RCurl Chicago: data.table matrixStats MASS Hmisc Delaporte methods grDevices graphics stats utils Rmixmod: Rcpp methods RcppEigen HiveR: grid plyr jpeg png RColorBrewer utils stats rgl tcltk csdR: WGCNA glue RhpcBLASctl matrixStats Rcpp pastecs: boot stats graphics utils grDevices RMallow: combinat nipalsMCIA: ComplexHeatmap dplyr fgsea ggplot2 graphics grid methods MultiAssayExperiment SummarizedExperiment pracma rlang RSpectra scales stats ModCon: data.table parallel utils stats hgu133afrmavecs: MGFM: AnnotationDbi annotate ggh4x: ggplot2 grid gtable scales vctrs rlang lifecycle stats cli RcppGSL: Rcpp stats GenomeInfoDb: methods BiocGenerics S4Vectors IRanges stats stats4 utils RCurl GenomeInfoDbData MGFR: biomaRt annotate SmoothWin: nlme Rfast PAIRADISE: nloptr SummarizedExperiment S4Vectors stats methods abind BiocParallel gridSVG: grDevices graphics utils methods grid jsonlite XML FLAMES: basilisk bambu Biostrings BiocGenerics circlize ComplexHeatmap cowplot dplyr DropletUtils GenomicRanges GenomicFeatures GenomicAlignments GenomeInfoDb ggplot2 ggbio grid gridExtra igraph jsonlite magrittr Matrix parallel reticulate Rsamtools rtracklayer RColorBrewer SingleCellExperiment SummarizedExperiment scater S4Vectors scuttle stats scran stringr MultiAssayExperiment tidyr utils withr zlibbioc future methods Rcpp Rhtslib R.utils: R.oo methods utils tools R.methodsS3 partykit: graphics grid libcoin mvtnorm grDevices stats utils survival Formula inum rpart stopwords: ISOcodes BiocParallel: methods stats utils futile.logger parallel snow codetools BH cpp11 CompoundDb: methods AnnotationFilter S4Vectors BiocGenerics ChemmineR tibble jsonlite dplyr DBI dbplyr RSQLite Biobase ProtGenerics xml2 IRanges Spectra MsCoreUtils MetaboCoreUtils BiocParallel TENxVisiumData: ExperimentHub SpatialExperiment utils rWikiPathways: httr utils XML rjson data.table RCurl dplyr tidyr readr stringr purrr lubridate treemap: colorspace data.table ggplot2 grid gridBase igraph methods RColorBrewer shiny HDF5Array: methods DelayedArray rhdf5 utils stats tools Matrix rhdf5filters BiocGenerics S4Vectors IRanges S4Arrays Rhdf5lib oppar: Biobase methods GSEABase GSVA log4r: ewceData: ExperimentHub oncoscanR: IRanges GenomicRanges magrittr readr S4Vectors methods utils metaMSdata: midasHLA: MultiAssayExperiment assertthat broom dplyr formattable HardyWeinberg kableExtra knitr magrittr methods stringi rlang S4Vectors stats SummarizedExperiment tibble utils qdapTools dendextend: utils stats datasets magrittr ggplot2 viridis BBCAnalyzer: SummarizedExperiment VariantAnnotation Rsamtools grDevices GenomicRanges IRanges Biostrings R6P: collections dplyr purrr R6 stringr tibble tidyr GoFKernel: stats KernSmooth crul: curl R6 urltools httpcode jsonlite mime ranger: Rcpp Matrix RcppEigen plotROC: ggplot2 methods grid gridSVG shiny plyr rlang seqminer: geNetClassifier: Biobase EBarrays minet methods e1071 graphics grDevices RLMM: graphics grDevices MASS stats utils CCP: gDRimport: assertthat BumpyMatrix checkmate CoreGx PharmacoGx data.table futile.logger gDRutils magrittr methods MultiAssayExperiment readxl rio S4Vectors stats stringi SummarizedExperiment tibble tools utils XML yaml openxlsx dearseq: CompQuadForm dplyr ggplot2 KernSmooth magrittr matrixStats methods patchwork parallel pbapply reshape2 rlang scattermore stats statmod survey tibble viridisLite lmodel2: flextable: stats utils grDevices graphics grid rmarkdown knitr htmltools rlang ragg officer gdtools xml2 data.table uuid magicaxis: grDevices graphics stats celestial MASS plotrix sm mapproj RANN deSolve: methods graphics grDevices stats NetSAM: seriation igraph tools WGCNA biomaRt methods AnnotationDbi doParallel foreach survival GO.db R2HTML DBI PAST: stats utils dplyr rlang iterators parallel foreach doParallel qvalue rtracklayer ggplot2 GenomicRanges S4Vectors CDI: matrixStats Seurat SeuratObject stats BiocParallel ggplot2 reshape2 grDevices ggsci SingleCellExperiment SummarizedExperiment methods bit64: bit utils methods stats CpGassoc: nlme methods SBGNview: pathview SBGNview.data Rdpack grDevices methods stats utils xml2 rsvg igraph rmarkdown knitr SummarizedExperiment AnnotationDbi httr KEGGREST bookdown ccrepe: infotheo superheat: dplyr ggplot2 gtable magrittr plyr scales ggdendro conicfit: pracma geigen GEOquery: methods Biobase readr xml2 dplyr data.table tidyr magrittr limma curl R.utils HybridMTest: Biobase fdrtool MASS survival stats alabaster.mae: MultiAssayExperiment alabaster.base methods alabaster.se S4Vectors sscu: Biostrings seqinr BiocGenerics changepoint: methods stats zoo LoomExperiment: S4Vectors SingleCellExperiment SummarizedExperiment methods rhdf5 BiocIO DelayedArray GenomicRanges HDF5Array Matrix stats stringr utils glmnet: Matrix methods utils foreach shape survival Rcpp RcppEigen iterativeBMA: BMA leaps Biobase bayestestR: insight datawizard graphics methods stats utils fGarch: fBasics timeDate timeSeries fastICA Matrix cvar graphics methods stats utils VaSP: ballgown IRanges GenomicRanges S4Vectors parallel matrixStats GenomicAlignments GenomeInfoDb Rsamtools cluster stats graphics methods syntenet: Rcpp BiocParallel GenomicRanges rlang Biostrings rtracklayer utils methods igraph stats grDevices RColorBrewer pheatmap ggplot2 ggnetwork intergraph networkD3 testthat metahdep: methods minqa: Rcpp BUS: minet stats infotheo cyanoFilter: Biobase flowCore flowDensity flowClust cytometree ggplot2 GGally graphics grDevices methods mrfDepth stats utils capushe: methods graphics MASS IlluminaDataTestFiles: mwcsr: methods igraph Rcpp mtbls2: mouse4302cdf: utils AnnotationDbi flowMatch: Rcpp methods flowCore Biobase gtrellis: grid IRanges GenomicRanges circlize GetoptLong grDevices utils DEGseq: qvalue methods graphics grDevices stats utils fmsb: pathifier: R.oo princurve fmrs: methods survival stats pingr: processx utils lintr: backports codetools cyclocomp digest glue knitr rex stats utils xml2 xmlparsedata gargle: cli fs glue httr jsonlite lifecycle openssl rappdirs rlang stats utils withr xopen: processx CellBench: SingleCellExperiment magrittr methods stats tibble utils assertthat BiocGenerics BiocFileCache BiocParallel dplyr rlang glue memoise purrr rappdirs tidyr tidyselect lubridate BSgenome.Hsapiens.UCSC.hg38.masked: GenomeInfoDb BSgenome BSgenome.Hsapiens.UCSC.hg38 MBttest: stats gplots gtools graphics base utils grDevices MGLM: methods stats parallel stats4 qpcrNorm: methods Biobase limma affy seqCNA: GLAD doSNOW adehabitatLT seqCNA.annot methods BSgenome.Ggallus.UCSC.galGal3: BSgenome GenVisR: methods AnnotationDbi biomaRt BiocGenerics Biostrings DBI GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales viridis data.table BSgenome GenomeInfoDb VariantAnnotation BGmix: KernSmooth MBAmethyl: msPurityData: AHMassBank: AnnotationHubData crisprViz: crisprBase crisprDesign BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicFeatures GenomicRanges grDevices Gviz IRanges methods S4Vectors ecodist: stats graphics igraph chron: graphics stats alluvial: iterativeBMAsurv: BMA leaps survival splines graphics grDevices stats utils msImpute: softImpute methods stats graphics pdist reticulate scran data.table FNN matrixStats limma mvtnorm tidyr dplyr MetaCyto: flowCore tidyr fastcluster ggplot2 metafor cluster FlowSOM grDevices graphics stats utils switchBox: pROC gplots PepsNMR: Matrix ptw ggplot2 gridExtra matrixStats reshape2 methods graphics stats aroma.light: stats R.methodsS3 R.oo R.utils matrixStats skmeans: slam clue cluster stats utils scPCA: stats methods assertthat tibble dplyr purrr stringr Rdpack matrixStats BiocParallel elasticnet sparsepca cluster kernlab origami RSpectra coop Matrix DelayedArray ScaledMatrix MatrixGenerics CellMapper: S4Vectors methods stats utils clustifyr: cowplot dplyr entropy fgsea ggplot2 Matrix rlang scales stringr tibble tidyr stats methods SingleCellExperiment SummarizedExperiment matrixStats S4Vectors proxy httr utils GOSemSim: AnnotationDbi GO.db methods rlang stats utils yulab.utils Rcpp tidybayes: methods ggdist dplyr tidyr ggplot2 coda rlang arrayhelpers tidyselect tibble magrittr posterior withr cli vctrs elitism: MASS stats vsclust: matrixStats limma parallel shiny qvalue grDevices stats MultiAssayExperiment graphics Rcpp chromhmmData: maxstat: exactRankTests mvtnorm stats graphics yesno: utils mCSEAdata: GenomicRanges cytoMEM: gplots tools flowCore grDevices stats utils matrixStats methods ptairData: rhdf5 signal stats graphics NetActivity: airway DelayedArray DelayedMatrixStats DESeq2 methods NetActivityData SummarizedExperiment utils FilterFFPE: foreach doParallel GenomicRanges IRanges Rsamtools parallel S4Vectors c3net: igraph gemma.R: magrittr glue memoise jsonlite data.table rlang lubridate utils stringr SummarizedExperiment Biobase tibble tidyr S4Vectors httr rappdirs bit64 assertthat digest iterators: utils RcppCCTZ: Rcpp BSgenome.Btaurus.UCSC.bosTau6: BSgenome ggplotify: ggplot2 graphics grDevices grid gridGraphics yulab.utils htmlwidgets: grDevices htmltools jsonlite knitr rmarkdown yaml receptLoss: dplyr ggplot2 magrittr tidyr SummarizedExperiment anytime: Rcpp BH fabia: Biobase methods graphics grDevices stats utils NormalyzerDE: vsn preprocessCore limma MASS ape car ggplot2 methods Biobase utils stats SummarizedExperiment matrixStats ggforce pairkat: SummarizedExperiment KEGGREST igraph data.table methods stats magrittr CompQuadForm tibble spikeLI: graphics grDevices stats utils oligo: BiocGenerics oligoClasses Biobase Biostrings affyio affxparser DBI ff graphics methods preprocessCore RSQLite splines stats stats4 utils zlibbioc websocket: R6 later cpp11 AsioHeaders CGHcall: impute DNAcopy methods Biobase CGHbase snowfall bigmelon: wateRmelon gdsfmt methods minfi Biobase methylumi stats utils GEOquery graphics BiocGenerics illuminaio multiHiCcompare: data.table dplyr HiCcompare edgeR BiocParallel qqman pheatmap methods GenomicRanges graphics stats utils pbapply GenomeInfoDbData GenomeInfoDb aggregation 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 genArise: locfit tkrplot methods graphics grDevices stats tcltk utils xtable Rfastp: Rcpp rjson ggplot2 reshape2 Rhtslib zlibbioc hiReadsProcessor: Biostrings GenomicAlignments BiocParallel hiAnnotator sonicLength dplyr BiocGenerics GenomicRanges readxl methods ecolitk: Biobase graphics methods netOmics: dplyr ggplot2 igraph magrittr minet purrr tibble tidyr AnnotationDbi GO.db RandomWalkRestartMH gprofiler2 methods stats psych: mnormt parallel stats graphics grDevices methods lattice nlme TMixClust: gss mvtnorm stats zoo cluster utils BiocParallel flexclust grDevices graphics Biobase SPEM corral: ggplot2 ggthemes grDevices gridExtra irlba Matrix methods MultiAssayExperiment pals reshape2 SingleCellExperiment SummarizedExperiment transport chromDraw: Rcpp GenomicRanges intrinsicDimension: yaImpute miniUI: shiny htmltools utils SQLDataFrame: dplyr dbplyr S4Vectors DBI lazyeval methods tools stats BiocGenerics RSQLite tibble glm2: stats MsExperiment: ProtGenerics methods S4Vectors 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BiocStyle Biobase ggplot2 WriteXLS gtools RColorBrewer limma grid gtable gridExtra biovizBase e1071 methods grDevices stats utils fastLiquidAssociation: methods LiquidAssociation parallel doParallel stats Hmisc utils WGCNA impute preprocessCore org.Dr.eg.db: methods AnnotationDbi hypeR: ggplot2 ggforce R6 magrittr dplyr purrr stats stringr scales rlang httr openxlsx htmltools reshape2 reactable msigdbr kableExtra rmarkdown igraph visNetwork shiny BiocStyle ExperimentHubData: utils BiocGenerics S4Vectors AnnotationHubData methods ExperimentHub BiocManager DBI httr curl pumadata: Biobase puma oligo summarytools: base64enc checkmate dplyr grDevices htmltools lubridate magick matrixStats methods pander pryr rapportools stats tcltk tibble tidyr utils DIAlignR: methods stats zoo data.table magrittr dplyr tidyr rlang mzR signal bit64 reticulate ggplot2 RSQLite DBI ape phangorn pracma RMSNumpress Rcpp RcppEigen cTRAP: AnnotationDbi AnnotationHub binr cowplot data.table dplyr DT fastmatch fgsea ggplot2 ggrepel graphics highcharter htmltools httr limma methods parallel pbapply purrr qs R.utils readxl reshape2 rhdf5 rlang scales shiny shinycssloaders stats tibble tools utils multiGSEA: magrittr graphite AnnotationDbi metaboliteIDmapping dplyr fgsea metap rappdirs rlang methods patrick: dplyr purrr rlang testthat tibble textclean: data.table english glue lexicon mgsub qdapRegex stringi textshape utils GBScleanR: SeqArray stats utils methods ggplot2 tidyr expm Rcpp RcppParallel gdsfmt singleCellTK: SummarizedExperiment SingleCellExperiment DelayedArray Biobase ape anndata AnnotationHub batchelor BiocParallel celldex colourpicker colorspace cowplot cluster ComplexHeatmap data.table DelayedMatrixStats DESeq2 dplyr DT ExperimentHub ensembldb 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 eds withr GSEABase R.utils zinbwave scRNAseq TENxPBMCData yaml rmarkdown magrittr scDblFinder metap VAM tibble rlang TSCAN TrajectoryUtils scuttle utils stats zellkonverter CLL: affy Biobase CMA: methods stats Biobase LineagePulse: BiocParallel circlize compiler ComplexHeatmap ggplot2 gplots grDevices grid knitr Matrix methods RColorBrewer SingleCellExperiment splines stats SummarizedExperiment utils hgu95av2probe: AnnotationDbi maps: graphics utils paintmap: VERSO: utils data.tree ape parallel Rfast stats GNET2: ggplot2 xgboost Rcpp reshape2 grid DiagrammeR methods stats matrixStats graphics SummarizedExperiment dplyr igraph grDevices utils alabaster.spatial: SpatialExperiment alabaster.base methods utils grDevices S4Vectors SummarizedExperiment jsonlite alabaster.sce rlecuyer: ggprism: digest ggplot2 glue grid gtable rlang scales stats tibble utils RGraph2js: utils whisker rjson digest graph 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tools utils Biobase Matrix MSnbase ggplot2 mzR GeuvadisTranscriptExpr: SnowballC: rslurm: whisker ToxicoGx: CoreGx SummarizedExperiment BiocGenerics S4Vectors Biobase BiocParallel ggplot2 tibble dplyr caTools downloader magrittr methods reshape2 tidyr data.table assertthat scales graphics grDevices parallel stats utils limma jsonlite formatR: scBFA: SingleCellExperiment SummarizedExperiment Seurat MASS zinbwave stats copula ggplot2 DESeq2 utils grid methods Matrix zip: PanViz: tidyr stringr dplyr tibble magrittr futile.logger utils easycsv rentrez igraph RColorBrewer data.table colorspace grDevices rlang methods RcppParallel: tidytree: ape dplyr lazyeval magrittr methods rlang tibble tidyr tidyselect yulab.utils pillar cli ccaPP: parallel pcaPP robustbase Rcpp RcppArmadillo transcriptR: methods BiocGenerics caret chipseq e1071 GenomicAlignments GenomicRanges GenomicFeatures GenomeInfoDb ggplot2 graphics grDevices IRanges pROC reshape2 Rsamtools rtracklayer S4Vectors stats utils geneRxCluster: GenomicRanges IRanges RefPlus: Biobase affy affyPLM preprocessCore R.oo: R.methodsS3 methods utils bezier: cisPath: methods utils diggit: Biobase methods ks viper parallel normr: methods stats utils grDevices parallel GenomeInfoDb GenomicRanges IRanges Rcpp qvalue bamsignals rtracklayer randPack: methods Biobase wordcloud: methods RColorBrewer Rcpp nullrangesData: ExperimentHub GenomicRanges InteractionSet utils ROntoTools: methods graph boot KEGGREST KEGGgraph Rgraphviz proDA: stats utils methods BiocGenerics SummarizedExperiment S4Vectors extraDistr SpacePAC: iPAC epiR: survival BiasedUrn pander methods sf lubridate zoo flextable officer marr: Rcpp SummarizedExperiment utils 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 ggfun ggnewscale 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 ggkegg: ggplot2 ggraph XML igraph tidygraph BiocFileCache GetoptLong data.table dplyr magick patchwork shadowtext stringr tibble org.Hs.eg.db methods utils stats AnnotationDbi grDevices gtable 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 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 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 AnnotationDbi clusterProfiler graph diptest cluster vioplot visNetwork vsn igraph FactoMineR factoextra dendextend parallel doParallel Mfuzz apcluster forcats readxl openxlsx multcomp purrr tibble knitr norm scales tidyverse cp4p imp4p lme4 dplyr limma preprocessCore stringr tidyr impute gplots grDevices reshape2 graphics stats methods ggplot2 RColorBrewer Matrix org.Sc.sgd.db tensorA: stats cfdnakit: Biobase dplyr GenomicRanges GenomeInfoDb ggplot2 IRanges magrittr PSCBS QDNAseq Rsamtools utils S4Vectors stats rlang 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 decoupleR 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 rlang 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 Rcpp RcppArmadillo 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 utils org.Xl.eg.db: methods AnnotationDbi 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 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 stats utils TOAST: EpiDISH limma nnls quadprog stats methods SummarizedExperiment corpcor doParallel parallel ggplot2 tidyr GGally idiogram: methods Biobase annotate plotrix ggbump: ggplot2 dplyr purrr tidyr 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 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 gRain: methods gRbase igraph stats4 broom magrittr Rcpp RcppArmadillo RcppEigen MCMCprecision: Rcpp parallel utils stats Matrix combinat RcppArmadillo RcppProgress 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 DFP: methods Biobase tomoda: methods stats grDevices reshape2 Rtsne umap RColorBrewer ggplot2 ggrepel SummarizedExperiment progress: crayon hms prettyunits R6 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 safetensors jsonlite dada2: Rcpp methods Biostrings ggplot2 reshape2 ShortRead RcppParallel parallel IRanges XVector BiocGenerics loo: checkmate matrixStats parallel posterior stats gDNAinRNAseqData: RCurl XML ExperimentHub BiocGenerics Rsamtools 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 BiocSingular PCAtools parallelDist ComplexHeatmap circlize grid scales RColorBrewer utils rlang Rfast stringr Seurat umap 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 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 SingleCellExperiment SummarizedExperiment SeuratObject ks Matrix stats methods ggrastr 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: cli glue httr lifecycle magrittr rlang selectr tibble xml2 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 hicVennDiagram: InteractionSet rtracklayer ggplot2 ComplexUpset reshape2 eulerr S4Vectors methods utils htmlwidgets svglite RegionalST: stats grDevices utils ggplot2 dplyr scater gridExtra BayesSpace fgsea magrittr SingleCellExperiment RColorBrewer Seurat S4Vectors tibble TOAST assertthat colorspace shiny SummarizedExperiment 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: methods graphics utils stats 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 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 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: iSEEpathways: iSEE ggplot2 methods S4Vectors shiny shinyWidgets stats SummarizedExperiment 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 rngWELL: 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 scatterplot3d stats utils CNVgears: data.table ggplot2 MANOR: GLAD graphics grDevices stats utils GEOexplorer: shiny limma Biobase plotly enrichR DT XML httr sva xfun edgeR htmltools factoextra heatmaply pheatmap scales shinyHeatmaply shinybusy ggplot2 stringr umap GEOquery impute grDevices stats graphics markdown knitr utils xml2 R.utils readxl shinycssloaders car 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 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 rdist: Rcpp methods RcppArmadillo apcluster: Rcpp methods Matrix stats graphics grDevices gDRtestData: checkmate mfa: methods stats ggplot2 Rcpp dplyr ggmcmc MCMCpack MCMCglmm coda magrittr tibble Biobase kableExtra: knitr magrittr stringr xml2 rmarkdown scales viridisLite stats grDevices htmltools rstudioapi tools 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 deSolve CNORode 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 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timeOmics: mixOmics dplyr tidyr tibble purrr magrittr ggplot2 stringr ggrepel lmtest plyr bcSeq: Rcpp Matrix Biostrings flowMeans: Biobase graphics grDevices methods rrcov stats feature flowCore evaluate: methods clValid: cluster methods class scDDboost: ggplot2 Rcpp RcppEigen EBSeq BiocParallel mclust SingleCellExperiment cluster Oscope SummarizedExperiment stats methods BH HiContactsData: ExperimentHub BiocFileCache AnnotationHub rebook: utils methods knitr rmarkdown CodeDepends dir.expiry filelock BiocStyle QuaternaryProd: Rcpp dplyr yaml strandCheckR: dplyr magrittr GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools S4Vectors grid BiocGenerics ggplot2 reshape2 stats gridExtra TxDb.Hsapiens.UCSC.hg38.knownGene methods stringr rmarkdown MAQCsubset: affy Biobase lumi methods DNABarcodeCompatibility: dplyr tidyr numbers purrr stringr DNABarcodes stats utils methods SIM: quantreg graphics stats globaltest quantsmooth TENxPBMCData: SingleCellExperiment HDF5Array AnnotationHub 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SummarizedExperiment epivizrData: methods epivizrServer Biobase S4Vectors GenomicRanges SummarizedExperiment OrganismDbi GenomicFeatures GenomeInfoDb IRanges ensembldb clippda: limma statmod rgl lattice scatterplot3d graphics grDevices stats utils Biobase tools methods ExCluster: Rsubread GenomicRanges rtracklayer matrixStats IRanges stats methods grDevices graphics utils affyContam: tools methods utils Biobase affy affydata BASiCStan: BASiCS rstan methods glmGamPoi scran scuttle stats utils SingleCellExperiment SummarizedExperiment Rcpp RcppParallel rstantools BH RcppEigen StanHeaders base64: openssl Seurat: methods SeuratObject cluster cowplot fastDummies fitdistrplus future future.apply generics ggplot2 ggrepel ggridges graphics grDevices grid httr ica igraph irlba jsonlite KernSmooth leiden lifecycle lmtest MASS Matrix matrixStats miniUI patchwork pbapply plotly png progressr purrr RANN RColorBrewer Rcpp RcppAnnoy RcppHNSW reticulate rlang ROCR RSpectra Rtsne scales scattermore 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grid gtable isoband lifecycle MASS mgcv rlang scales stats tibble vctrs withr MsBackendMsp: Spectra BiocParallel S4Vectors IRanges MsCoreUtils methods stats mltools: data.table Matrix methods stats clusterStab: Biobase methods colorRamps: Affymoe4302Expr: Rhdf5lib: vulcan: ChIPpeakAnno TxDb.Hsapiens.UCSC.hg19.knownGene zoo GenomicRanges S4Vectors viper DiffBind locfit wordcloud csaw gplots stats utils caTools graphics DESeq2 Biobase doubletrouble: syntenet GenomicRanges Biostrings mclust MSA2dist ggplot2 rlang stats utils AnnotationDbi GenomicFeatures BiocParallel alphahull: ggplot2 interp R.utils sgeostat spatstat.geom spatstat.random splancs textstem: koRpus.lang.en dplyr hunspell koRpus lexicon quanteda SnowballC stats stringi textclean textshape utils derfinderData: globalSeq: janitor: dplyr hms lifecycle lubridate magrittr purrr rlang stringi stringr snakecase tidyselect tidyr BiocSingular: BiocGenerics S4Vectors Matrix methods utils DelayedArray BiocParallel ScaledMatrix irlba 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IRanges Rbowtie readr stats stringr utils speedglm: Matrix MASS biglm methods stats CINdex: GenomicRanges bitops gplots grDevices som dplyr gridExtra png stringr S4Vectors IRanges GenomeInfoDb graphics stats utils multiClust: mclust ctc survival cluster dendextend amap graphics grDevices NBAMSeq: SummarizedExperiment S4Vectors DESeq2 mgcv BiocParallel genefilter methods stats easylift: GenomicRanges BiocFileCache rtracklayer GenomeInfoDb R.utils tools methods GEWIST: car a4Core: Biobase glmnet methods stats BSgenome.Mmusculus.UCSC.mm10: BSgenome IntEREst: GenomicRanges Rsamtools SummarizedExperiment edgeR S4Vectors GenomicFiles seqLogo Biostrings GenomicFeatures IRanges seqinr graphics grDevices stats utils grid methods DBI RMySQL GenomicAlignments BiocParallel BiocGenerics DEXSeq DESeq2 Spaniel: Seurat SingleCellExperiment SummarizedExperiment dplyr methods ggplot2 scater scran igraph shiny jpeg magrittr utils S4Vectors DropletUtils jsonlite png BioNetStat: shiny igraph shinyBS 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GenomicFeatures AnnotationDbi omicRexposome: Biobase stats utils grDevices graphics methods rexposome limma sva ggplot2 ggrepel PMA omicade4 gridExtra MultiDataSet SmartSVA isva parallel SummarizedExperiment stringr ade4: graphics grDevices methods stats utils MASS pixmap sp Rcpp RcppArmadillo opencpu: evaluate httpuv knitr jsonlite remotes sys webutils curl rappdirs rlang vctrs methods zip mime protolite brew openssl GeoDiff: Biobase Matrix robust plyr lme4 Rcpp withr methods graphics stats testthat GeomxTools NanoStringNCTools RcppArmadillo roptim BiocVersion: gridpattern: glue grDevices grid memoise png rlang sf utils gbm: lattice parallel survival blastula: base64enc commonmark curl digest dplyr fs getPass here htmltools httr jsonlite magrittr mime rlang rmarkdown stringr uuid a4Preproc: BiocGenerics Biobase mclust: stats utils graphics grDevices NADA: methods survival SNPlocs.Hsapiens.dbSNP155.GRCh37: BSgenome methods utils BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges girafe: methods BiocGenerics S4Vectors Rsamtools intervals ShortRead genomeIntervals grid Biobase Biostrings graphics grDevices stats utils IRanges SNPlocs.Hsapiens.dbSNP155.GRCh38: BSgenome methods utils BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges pdftools: Rcpp qpdf DEsubs: locfit graph igraph RBGL circlize limma edgeR EBSeq NBPSeq stats grDevices graphics pheatmap utils ggplot2 Matrix jsonlite tools DESeq2 methods maftools: data.table grDevices methods RColorBrewer Rhtslib survival DNAcopy zlibbioc xtable: stats utils HDInterval: BSgenome.Scerevisiae.UCSC.sacCer1: BSgenome KernSmooth: stats BSgenome.Scerevisiae.UCSC.sacCer2: BSgenome biganalytics: stats utils bigmemory foreach biglm methods Rcpp BH BSgenome.Scerevisiae.UCSC.sacCer3: BSgenome CoreGx: BiocGenerics SummarizedExperiment Biobase S4Vectors MultiAssayExperiment MatrixGenerics piano BiocParallel parallel BumpyMatrix checkmate methods stats utils graphics grDevices lsa data.table crayon glue rlang bench chihaya: DelayedArray methods Matrix rhdf5 Rcpp HDF5Array Rhdf5lib goftest: stats stringfish: Rcpp RcppParallel fst: fstcore Rcpp RTCGA.mutations: RTCGA GRridge: penalized Iso survival methods graph stats glmnet mvtnorm lambda.r: formatR breakpointR: GenomicRanges cowplot breakpointRdata methods utils grDevices stats S4Vectors GenomeInfoDb IRanges Rsamtools GenomicAlignments ggplot2 BiocGenerics gtools doParallel foreach MBQN: stats graphics utils limma SummarizedExperiment preprocessCore BiocFileCache rappdirs xml2 RCurl ggplot2 PairedData rmarkdown analogue: vegan mgcv MASS stats graphics grid brglm princurve lattice drosophila2probe: AnnotationDbi rmelting: Rdpack rJava evaluomeR: SummarizedExperiment MultiAssayExperiment cluster fpc randomForest flexmix corrplot grDevices graphics reshape2 ggplot2 ggdendro plotrix stats matrixStats Rdpack MASS class prabclus mclust kableExtra rbsurv: Biobase survival ttgsea: keras tm text2vec tokenizers textstem stopwords data.table purrr 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MatrixGenerics Matrix methods purrr GSEABase data.table zenith mashr ashr dplyr BiocParallel ggbeeswarm S4Vectors IRanges irlba limma metafor remaCor broom tidyr rlang BiocGenerics DelayedArray gtools reshape2 ggrepel scattermore Rcpp lme4 MASS Rdpack utils stats beachmat imputeLCMD: tmvtnorm norm pcaMethods impute INPower: mvtnorm shinytitle: shiny SEtools: SummarizedExperiment sechm BiocParallel Matrix DESeq2 S4Vectors data.table edgeR openxlsx pheatmap stats circlize methods sva calibrate: MASS methInheritSim: methylKit GenomicRanges GenomeInfoDb parallel BiocGenerics S4Vectors methods stats IRanges msm bigsparser: Rcpp bigassertr methods Matrix rmio RcppEigen mAPKL: Biobase multtest clusterSim apcluster limma e1071 AnnotationDbi methods parmigene igraph reactome.db celldex: SummarizedExperiment utils ExperimentHub AnnotationHub AnnotationDbi S4Vectors DelayedArray DelayedMatrixStats DuoClustering2018: ExperimentHub utils magrittr dplyr tidyr mclust ggplot2 purrr reshape2 viridis ggthemes stats methods TCGAutils: AnnotationDbi BiocGenerics BiocBaseUtils GenomeInfoDb GenomicFeatures GenomicRanges GenomicDataCommons IRanges methods MultiAssayExperiment RaggedExperiment rvest S4Vectors stats stringr SummarizedExperiment utils xml2 carData: ChemoSpec: ChemoSpecUtils stats utils grDevices reshape2 readJDX patchwork ggplot2 plotly magrittr synergyfinder: drc reshape2 tidyverse dplyr tidyr purrr furrr ggplot2 ggforce grid vegan gstat sp methods SpatialExtremes ggrepel kriging plotly stringr future mice lattice nleqslv stats graphics grDevices magrittr pbapply metR ITALICSData: hexbin: methods lattice grid graphics grDevices stats utils tfprobability: tensorflow reticulate keras magrittr doBy: methods broom Deriv dplyr ggplot2 MASS Matrix magrittr microbenchmark pbkrtest tibble ggfortify: methods ggplot2 dplyr tidyr gridExtra grid scales stringr tibble TSAR: dplyr ggplot2 ggpubr magrittr mgcv readxl stringr tidyr utils shiny plotly shinyjs jsonlite rhandsontable 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magrittr matrixStats methods MultiAssayExperiment purrr R6 Rdpack rlang stats S4Vectors tidyr utils BiocPkgTools: htmlwidgets BiocFileCache BiocManager biocViews tibble magrittr methods rlang stringr rvest dplyr xml2 readr httr htmltools DT tools utils igraph jsonlite gh RBGL graph rorcid org.EcSakai.eg.db: methods AnnotationDbi MBA: BH RUVnormalizeData: Biobase ClusterSignificance: methods pracma princurve scatterplot3d RColorBrewer grDevices graphics utils stats ggraph: ggplot2 dplyr ggforce grid igraph scales MASS ggrepel utils stats viridis rlang tidygraph graphlayouts withr cli vctrs lifecycle memoise cpp11 HSMMSingleCell: rstan: StanHeaders methods stats4 inline gridExtra Rcpp RcppParallel loo pkgbuild QuickJSR ggplot2 RcppEigen BH SNFtool: ExPosition alluvial babelgene: dplyr methods rlang bigassertr: shinyFeedback: fontawesome htmltools jsonlite shiny CardinalIO: matter ontologyIndex methods S4Vectors stats utils tools interactiveDisplay: methods BiocGenerics grid interactiveDisplayBase shiny RColorBrewer ggplot2 reshape2 plyr gridSVG XML Category AnnotationDbi MoonlightR: doParallel foreach parmigene randomForest SummarizedExperiment gplots circlize RColorBrewer HiveR clusterProfiler DOSE Biobase limma grDevices graphics TCGAbiolinks GEOquery stats RISmed grid utils RWeka: RWekajars rJava graphics stats utils grid here: rprojroot attempt: rlang SingleCellExperiment: SummarizedExperiment methods utils stats S4Vectors BiocGenerics GenomicRanges DelayedArray GENLIB: Rcpp kinship2 methods bootstrap Matrix lattice quadprog foreach parallel doParallel BH HiCool: HiCExperiment BiocIO S4Vectors GenomicRanges IRanges InteractionSet vroom basilisk reticulate rmarkdown rmdformats plotly dplyr stringr sessioninfo utils ggm: methods BiocManager graph igraph proteinProfiles: graphics stats BSgenome.Rnorvegicus.UCSC.rn5.masked: BSgenome BSgenome.Rnorvegicus.UCSC.rn5 KnowSeq: cqn stringr methods ggplot2 jsonlite kernlab rlist rmarkdown reshape2 e1071 randomForest caret XML praznik R.utils httr sva edgeR limma grDevices graphics stats utils Hmisc gridExtra epiNEM: BoolNet e1071 gtools stats igraph utils lattice latticeExtra RColorBrewer pcalg minet grDevices graph mnem latex2exp Xeva: methods stats utils BBmisc Biobase grDevices ggplot2 scales ComplexHeatmap parallel doParallel Rmisc grid nlme PharmacoGx downloader LSD: transport: grDevices graphics methods stats Rcpp data.table RcppEigen ScaledMatrix: methods Matrix S4Vectors DelayedArray annmap: methods GenomicRanges DBI RMySQL digest Biobase grid lattice Rsamtools genefilter IRanges BiocGenerics funtooNorm: pls matrixStats minfi methods IlluminaHumanMethylation450kmanifest IlluminaHumanMethylation450kanno.ilmn12.hg19 GenomeInfoDb grDevices graphics stats SQUADD: graphics grDevices methods RColorBrewer stats utils spBayes: coda sp magic Formula Matrix koRpus.lang.en: koRpus methods sylly.en callr: processx R6 utils smatr: MCL: expm scanMiR: Biostrings GenomicRanges IRanges data.table BiocParallel methods GenomeInfoDb S4Vectors ggplot2 stats stringi utils graphics grid seqLogo cowplot BSgenome.Rnorvegicus.UCSC.rn4: BSgenome functional: TH.data: survival MASS BSgenome.Rnorvegicus.UCSC.rn5: BSgenome BSgenome.Rnorvegicus.UCSC.rn6: BSgenome CTSV: stats pscl qvalue BiocParallel methods knitr SpatialExperiment SummarizedExperiment BSgenome.Rnorvegicus.UCSC.rn7: BSgenome tRNA: GenomicRanges Structstrings stringr S4Vectors methods BiocGenerics IRanges XVector Biostrings Modstrings ggplot2 scales AnnotationHub: BiocGenerics BiocFileCache utils methods grDevices RSQLite BiocManager BiocVersion curl rappdirs AnnotationDbi S4Vectors httr yaml dplyr interactiveDisplayBase Rlabkey: httr jsonlite Rcpp decompTumor2Sig: ggplot2 methods Matrix quadprog GenomicRanges stats GenomicFeatures Biostrings BiocGenerics S4Vectors plyr utils graphics BSgenome.Hsapiens.UCSC.hg19 TxDb.Hsapiens.UCSC.hg19.knownGene VariantAnnotation SummarizedExperiment ggseqlogo gridExtra data.table GenomeInfoDb readxl BSgenome.Mmusculus.UCSC.mm8.masked: BSgenome BSgenome.Mmusculus.UCSC.mm8 SpatialExtremes: maps fields base64enc: infinityFlow: flowCore stats grDevices utils graphics pbapply matlab png raster grid uwot gtools Biobase generics parallel methods xgboost singscore: methods stats graphics ggplot2 grDevices ggrepel GSEABase plotly tidyr plyr magrittr reshape edgeR RColorBrewer Biobase BiocParallel SummarizedExperiment matrixStats reshape2 S4Vectors DirichletMultinomial: S4Vectors IRanges stats4 methods BiocGenerics biodbLipidmaps: biodb lifecycle R6 cobs: SparseM quantreg grDevices graphics splines stats methods HTMLUtils: R2HTML methods grDevices Gviz: methods S4Vectors IRanges GenomicRanges grid XVector rtracklayer lattice RColorBrewer biomaRt AnnotationDbi Biobase GenomicFeatures ensembldb BSgenome Biostrings biovizBase Rsamtools latticeExtra matrixStats GenomicAlignments GenomeInfoDb BiocGenerics digest graphics grDevices stats utils BayesKnockdown: stats Biobase CyTOFpower: CytoGLMM diffcyt DT dplyr ggplot2 magrittr methods rlang stats shiny shinyFeedback shinyjs shinyMatrix SummarizedExperiment tibble tidyr htmlTable: stringr knitr magrittr methods checkmate htmlwidgets htmltools rstudioapi ggpp: ggplot2 stats grid grDevices rlang magrittr glue gridExtra scales tibble dplyr xts zoo MASS polynom lubridate stringr enrichR: httr curl rjson ggplot2 WriteXLS Delaporte: stats parallel zinbwave: methods SummarizedExperiment SingleCellExperiment BiocParallel softImpute stats genefilter edgeR Matrix mouse4302frmavecs: snow: utils rapidjsonr: GMRP: stats utils graphics grDevices diagram plotrix base GenomicRanges AmpAffyExample: affy msPurity: Rcpp plyr dplyr dbplyr magrittr foreach parallel doSNOW stringr mzR reshape2 fastcluster ggplot2 DBI RSQLite MEB: e1071 edgeR scater stats wrswoR SummarizedExperiment SingleCellExperiment CNVrd2: methods VariantAnnotation parallel rjags ggplot2 gridExtra DNAcopy IRanges Rsamtools RIVER: glmnet pROC ggplot2 graphics stats Biobase methods utils BSgenome.Mmusculus.UCSC.mm9.masked: BSgenome BSgenome.Mmusculus.UCSC.mm9 coda: lattice flowStats: BiocGenerics MASS flowCore flowWorkspace ncdfFlow flowViz fda Biobase methods grDevices graphics stats cluster utils KernSmooth lattice ks RColorBrewer rrcov corpcor mnormt clue hapmap100kxba: methylInheritance: methylKit BiocParallel GenomicRanges IRanges S4Vectors methods parallel ggplot2 gridExtra rebus logicFS: LogicReg mcbiopi survival graphics methods stats microbiome: phyloseq ggplot2 Biostrings compositions dplyr reshape2 Rtsne scales stats tibble tidyr utils vegan furrr: future globals lifecycle purrr rlang vctrs phylobase: ade4 ape Rcpp rncl grid methods stats RNeXML fstcore: Rcpp biobroom: broom dplyr tidyr Biobase alabaster.ranges: GenomicRanges alabaster.base methods utils S4Vectors BiocGenerics IRanges GenomeInfoDb agricolae: MASS nlme cluster AlgDesign graphics PureCN: DNAcopy VariantAnnotation GenomicRanges IRanges RColorBrewer S4Vectors data.table grDevices graphics stats utils SummarizedExperiment GenomeInfoDb GenomicFeatures Rsamtools Biobase Biostrings BiocGenerics rtracklayer ggplot2 gridExtra futile.logger VGAM tools methods mclust rhdf5 Matrix config: yaml odseq: msa kebabs mclust methylPipe: methods grDevices graphics stats utils GenomicRanges SummarizedExperiment Rsamtools marray gplots IRanges BiocGenerics Gviz GenomicAlignments Biostrings parallel data.table GenomeInfoDb S4Vectors rGenomeTracks: imager reticulate methods rGenomeTracksData ClusterR: Rcpp graphics grDevices utils stats gmp ggplot2 lifecycle RcppArmadillo exomePeak2: SummarizedExperiment Rsamtools GenomicAlignments GenomicRanges GenomicFeatures DESeq2 ggplot2 mclust BSgenome Biostrings GenomeInfoDb BiocParallel IRanges S4Vectors rtracklayer methods stats utils BiocGenerics magrittr speedglm splines printr: knitr Mfuzz: Biobase e1071 tcltk tkWidgets sendmailR: base64enc RMSNumpress: Rcpp bambu: SummarizedExperiment S4Vectors BSgenome IRanges BiocGenerics BiocParallel data.table dplyr tidyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges stats Rsamtools methods Rcpp xgboost RcppArmadillo strex: stringr checkmate lifecycle magrittr rlang stats stringi utils iChip: limma echarts4r: htmlwidgets dplyr purrr countrycode broom shiny scales corrplot htmltools jsonlite rstudioapi SAVER: glmnet foreach methods iterators doParallel Matrix sscore: affy affyio regsplice: glmnet SummarizedExperiment S4Vectors limma edgeR stats pbapply utils methods rawrr: grDevices graphics stats utils bookdown: htmltools knitr rmarkdown jquerylib xfun tinytex yaml edgeR: limma methods graphics stats utils locfit Rcpp ggsc: Rcpp RcppParallel cli dplyr ggplot2 grDevices grid methods rlang scattermore stats Seurat SingleCellExperiment SummarizedExperiment tidydr tidyr tibble utils yulab.utils RcppArmadillo gscreend: SummarizedExperiment nloptr fGarch methods BiocParallel graphics OSCA.intro: batchelor BiocFileCache BiocManager bluster DropletTestFiles DropletUtils gridExtra knitr LoomExperiment R.utils readxl rebook rmarkdown rtracklayer scater scran scRNAseq scuttle SingleCellExperiment uwot zellkonverter Guitar: GenomicFeatures rtracklayer AnnotationDbi GenomicRanges magrittr ggplot2 methods stats utils knitr dplyr pickgene: graphics grDevices MASS stats utils dirmult: gld: stats graphics e1071 lmom MineICA: methods BiocGenerics Biobase plyr ggplot2 scales foreach xtable biomaRt gtools GOstats cluster marray mclust RColorBrewer colorspace igraph Rgraphviz graph annotate Hmisc fastICA JADE AnnotationDbi lumi fpc lumiHumanAll.db sparseMatrixStats: MatrixGenerics Rcpp Matrix matrixStats methods RcppArmadillo: Rcpp stats utils methods isa2: methods grDevices lattice stats utils akima: sp SVMDO: shiny shinyFiles shinytitle golem nortest e1071 BSDA data.table sjmisc klaR caTools caret survival DOSE AnnotationDbi org.Hs.eg.db dplyr SummarizedExperiment grDevices graphics stats utils TFBSTools: Biobase Biostrings 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