mongolite: jsonlite openssl mime seqplots: methods IRanges BSgenome digest rtracklayer GenomicRanges Biostrings shiny DBI RSQLite plotrix fields grid kohonen parallel GenomeInfoDb class S4Vectors ggplot2 reshape2 gridExtra jsonlite DT RColorBrewer Rsamtools GenomicAlignments BiocManager sendmailR: base64enc naivebayes: dbscan: Rcpp graphics stats flexmix: lattice graphics grid grDevices methods modeltools nnet stats stats4 utils cn.mops: methods utils stats graphics parallel GenomicRanges BiocGenerics Biobase IRanges Rsamtools GenomeInfoDb S4Vectors exomeCopy breakpointRdata: IMPCdata: rjson anota: qvalue multtest parallel: tools compiler RISmed: methods conumee: minfi IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno.ilm10b2.hg19 IlluminaHumanMethylationEPICmanifest methods stats DNAcopy rtracklayer GenomicRanges IRanges GenomeInfoDb TSRchitect: AnnotationHub BiocGenerics BiocParallel dplyr GenomicAlignments GenomeInfoDb GenomicRanges gtools IRanges methods readxl Rsamtools rtracklayer S4Vectors SummarizedExperiment tools utils gmodels: MASS gdata ModelMetrics: Rcpp data.table Rcsdp: methods S4Vectors: methods utils stats stats4 BiocGenerics TFBSTools: Biobase Biostrings BiocGenerics BiocParallel BSgenome caTools CNEr DirichletMultinomial GenomeInfoDb GenomicRanges gtools grid IRanges methods DBI RSQLite rtracklayer seqLogo S4Vectors TFMPvalue XML XVector parallel BufferedMatrix: methods rbsurv: Biobase survival seqbias: GenomicRanges Biostrings methods Rhtslib doParallel: foreach iterators parallel utils BiBitR: stats foreign methods utils viridis cluster dendextend lattice grDevices graphics randomcoloR biclust InteractionSet: GenomicRanges SummarizedExperiment methods Matrix Rcpp BiocGenerics S4Vectors IRanges GenomeInfoDb R2HTML: stats graphics utils grDevices methods contrast: nlme sandwich rms mBPCR: oligoClasses GWASTools Biobase graphics methods utils grDevices GSVAdata: Biobase GSEABase hgu95a.db patchwork: ggplot2 gtable grid stats grDevices utils graphics norm: TxDb.Ggallus.UCSC.galGal5.refGene: GenomicFeatures AnnotationDbi htmltools: utils digest grDevices base64enc rlang systemfonts: cpp11 AlgDesign: chipseq: methods BiocGenerics S4Vectors IRanges GenomicRanges ShortRead stats lattice AnnotationFuncs: AnnotationDbi DBI TCseq: edgeR BiocGenerics reshape2 GenomicRanges IRanges SummarizedExperiment GenomicAlignments Rsamtools e1071 cluster ggplot2 grid grDevices stats utils methods locfit spatialHeatmap: av DESeq2 edgeR WGCNA flashClust htmlwidgets genefilter ggplot2 ggdendro grImport grid gridExtra gplots igraph rsvg shiny dynamicTreeCut grDevices graphics ggplotify plotly rols stats SummarizedExperiment shinydashboard utils visNetwork methods xml2 yaml LowMACAAnnotation: AllelicImbalance: grid GenomicRanges SummarizedExperiment GenomicAlignments methods BiocGenerics AnnotationDbi BSgenome VariantAnnotation Biostrings S4Vectors IRanges Rsamtools GenomicFeatures Gviz lattice latticeExtra gridExtra seqinr GenomeInfoDb nlme splus2R: methods RaggedExperiment: GenomicRanges BiocGenerics GenomeInfoDb IRanges Matrix MatrixGenerics methods S4Vectors stats SummarizedExperiment genefu: survcomp mclust limma biomaRt iC10 AIMS amap impute snpStats: survival Matrix methods graphics grDevices stats utils BiocGenerics zlibbioc DEoptimR: stats diggitdata: Biobase methods viper MouseFM: httr curl GenomicRanges dplyr ggplot2 reshape2 scales gtools tidyr data.table jsonlite rlist GenomeInfoDb methods biomaRt stats IRanges TxDb.Rnorvegicus.UCSC.rn5.refGene: GenomicFeatures AnnotationDbi backports: hom.Dm.inp.db: methods AnnotationDbi compartmap: minfi Homo.sapiens mixOmics SummarizedExperiment GenomicRanges gtools parallel infotheo: diffuStats: grDevices stats methods Matrix MASS checkmate expm igraph Rcpp RcppArmadillo RcppParallel plyr precrec baseline: graphics SparseM grDevices stats methods limSolve tsne: CountClust: ggplot2 SQUAREM slam maptpx plyr cowplot gtools flexmix picante limma parallel reshape2 stats utils graphics grDevices tidySingleCellExperiment: SingleCellExperiment dplyr tibble tidyr ggplot2 plotly magrittr rlang purrr lifecycle methods utils S4Vectors tidyselect ellipsis pillar stringr cli fansi quantmod: xts zoo TTR methods curl ASpli: methods grDevices stats utils parallel edgeR limma AnnotationDbi GenomicRanges GenomicFeatures BiocGenerics IRanges GenomicAlignments Gviz S4Vectors Rsamtools BiocStyle igraph htmltools data.table UpSetR tidyr DT MASS grid graphics mcmc: stats PureCN: DNAcopy VariantAnnotation GenomicRanges IRanges RColorBrewer S4Vectors data.table grDevices graphics stats utils SummarizedExperiment GenomeInfoDb GenomicFeatures Rsamtools Biostrings BiocGenerics rtracklayer ggplot2 gridExtra futile.logger VGAM tools methods rhdf5 Matrix polyclip: clusterCrit: PrecisionTrialDrawer: graphics grDevices stats utils methods cgdsr parallel stringr reshape2 data.table RColorBrewer BiocParallel magrittr biomaRt XML httr jsonlite ggplot2 ggrepel grid S4Vectors IRanges GenomicRanges LowMACAAnnotation googleVis shiny shinyBS DT brglm matrixStats DrugVsDiseasedata: bridge: rama ChIPComp: GenomicRanges IRanges rtracklayer GenomeInfoDb S4Vectors Rsamtools limma BSgenome.Hsapiens.UCSC.hg19 BSgenome.Mmusculus.UCSC.mm9 BiocGenerics SBGNview.data: knitr rmarkdown bookdown SparseM: methods graphics stats utils drawer: htmltools magrittr glue bsplus utils shiny stringr tinytest: parallel utils RCircos: tenXplore: shiny restfulSE methods ontoProc SummarizedExperiment AnnotationDbi matrixStats org.Mm.eg.db stats utils Rsolnp: truncnorm parallel stats urca: methods nlme graphics stats googleVis: methods jsonlite utils animalcules: assertthat shiny shinyjs DESeq2 caret plotly ggplot2 rentrez reshape2 covr ape vegan dplyr magrittr MultiAssayExperiment SummarizedExperiment S4Vectors XML forcats scales lattice glmnet tsne DMwR plotROC DT reactable utils limma methods stats tibble biomformat umap Matrix GUniFrac genphen: Rcpp methods stats graphics rstan ranger parallel foreach doParallel e1071 Biostrings rPref vegan: permute lattice MASS cluster mgcv msPurity: Rcpp plyr dplyr dbplyr magrittr foreach parallel doSNOW stringr mzR reshape2 fastcluster ggplot2 DBI RSQLite uuid jsonlite goTools: GO.db AnnotationDbi graphics grDevices tidybulk: tibble readr dplyr magrittr tidyr stringr rlang purrr preprocessCore stats parallel utils lifecycle scales SummarizedExperiment methods aplot: ggplot2 patchwork magrittr methods tidygraph: tibble dplyr igraph magrittr utils rlang R6 Rcpp tools stats tidyr pillar CCP: ggExtra: colourpicker ggplot2 grDevices grid gtable miniUI scales shiny shinyjs utils R6 impute: sevenC: InteractionSet rtracklayer BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors readr purrr data.table boot methods biomartr: biomaRt Biostrings curl tibble jsonlite data.table dplyr readr downloader RCurl XML httr stringr purrr R.utils philentropy fs KinSwingR: data.table BiocParallel sqldf stats grid grDevices kml: methods clv longitudinalData graper: Matrix Rcpp stats ggplot2 methods cowplot matrixStats RcppArmadillo BH furrr: future ellipsis globals lifecycle purrr rlang vctrs simulatorZ: Biobase SummarizedExperiment survival CoxBoost BiocGenerics graphics stats gbm Hmisc GenomicRanges methods DAPARdata: utils knitr MSnbase rmutil: MoonlightR: doParallel foreach parmigene randomForest SummarizedExperiment gplots circlize RColorBrewer HiveR clusterProfiler DOSE Biobase limma grDevices graphics TCGAbiolinks GEOquery stats RISmed grid utils assertive.matrices: assertive.base cMAP: MSstatsTMTPTM: dplyr gridExtra stringr reshape2 stats utils ggplot2 grDevices graphics MSstatsTMT Rcpp sitePath: RColorBrewer Rcpp ape aplot ggplot2 ggrepel ggtree graphics grDevices gridExtra methods parallel seqinr stats tidytree utils yaqcaffy: simpleaffy methods stats4 PolynomF: graphics grDevices stats Rcpp methods antiProfilesData: Biobase metap: lattice Rdpack TFisher mutoss mathjaxr flowFit: flowCore flowViz graphics kza methods minpack.lm gplots diagram: shape stats graphics blacksheepr: grid stats grDevices utils circlize viridis RColorBrewer ComplexHeatmap SummarizedExperiment pasilla MinimumDistance: VanillaICE methods BiocGenerics MatrixGenerics Biobase S4Vectors IRanges GenomeInfoDb GenomicRanges SummarizedExperiment oligoClasses DNAcopy ff foreach matrixStats lattice data.table grid stats utils GCSConnection: Rcpp httr googleAuthR googleCloudStorageR methods jsonlite utils LRBase.Hsa.eg.db: LRBaseDbi RSQLite packFinder: Biostrings GenomicRanges kmer ape methods IRanges S4Vectors ppiData: graph AnnotationDbi BUS: minet stats infotheo BridgeDbR: rJava curl ecoliLeucine: affy ecolicdf uSORT: tcltk igraph Matrix RANN RSpectra VGAM gplots parallel plyr methods cluster Biobase fpc BiocGenerics monocle grDevices graphics stats utils randomForest: stats assertive.strings: assertive.base assertive.types stringi sandwich: stats utils zoo SMAD: RcppAlgos magrittr dplyr stats tidyr utils Rcpp dplyr: ellipsis generics glue lifecycle magrittr methods R6 rlang tibble tidyselect utils vctrs pillar iChip: limma CGHcall: impute DNAcopy methods Biobase CGHbase snowfall RCASPAR: ccdrAlgorithm: sparsebnUtils Rcpp stats utils DominoEffect: biomaRt data.table utils stats Biostrings SummarizedExperiment VariantAnnotation AnnotationDbi GenomeInfoDb IRanges GenomicRanges methods SMAP: methods reldist: mgcv Hmisc SPAtest: Linnorm: Rcpp RcppArmadillo fpc vegan mclust apcluster ggplot2 ellipse limma utils statmod MASS igraph grDevices graphics fastcluster ggdendro zoo stats amap Rtsne gmodels GeneAccord: biomaRt caTools dplyr ggplot2 graphics grDevices gtools ggpubr magrittr maxLik RColorBrewer reshape2 stats tibble utils GSRI: fdrtool methods graphics stats utils genefilter Biobase GSEABase les caTools: bitops msigdbr: babelgene dplyr magrittr rlang tibble tidyselect ImmuneSpaceR: utils R6 data.table curl httr Rlabkey Biobase pheatmap ggplot2 scales stats gplots plotly heatmaply jsonlite rmarkdown preprocessCore flowCore flowWorkspace digest BSgenome.Hsapiens.UCSC.hg19.masked: BSgenome BSgenome.Hsapiens.UCSC.hg19 prettydoc: rmarkdown htm2txt: ssize: gdata xtable fibroEset: Biobase hapmap100kxba: Wrench: limma matrixStats locfit stats graphics lapmix: stats Biobase graphics grDevices methods tools utils sparsebnUtils: Matrix stats utils methods nnet miscTools: digest scPCA: stats methods assertthat tibble dplyr purrr stringr Rdpack matrixStats BiocParallel elasticnet sparsepca cluster kernlab origami RSpectra coop Matrix DelayedArray CellNOptR: RBGL graph methods hash RCurl Rgraphviz XML ggplot2 igraph stringi stringr BSgenome.Hsapiens.UCSC.hg18.masked: BSgenome BSgenome.Hsapiens.UCSC.hg18 GenomicAlignments: methods BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges SummarizedExperiment Biostrings Rsamtools utils stats BiocParallel stable: rmutil stabledist frmaTools: affy Biobase DBI methods preprocessCore stats utils GDCRNATools: shiny jsonlite rjson XML limma edgeR DESeq2 clusterProfiler DOSE org.Hs.eg.db biomaRt survival survminer pathview ggplot2 gplots DT GenomicDataCommons BiocParallel QuasR: parallel GenomicRanges Rbowtie methods grDevices graphics utils BiocGenerics S4Vectors IRanges BiocManager Biobase Biostrings BSgenome Rsamtools GenomicFeatures ShortRead GenomicAlignments BiocParallel GenomeInfoDb rtracklayer GenomicFiles Rhisat2 AnnotationDbi Rhtslib Rmpfr: gmp stats utils methods plrs: Biobase BiocGenerics CGHbase graphics grDevices ic.infer marray methods quadprog Rcsdp stats stats4 utils appreci8R: shiny shinyjs DT VariantAnnotation BSgenome BSgenome.Hsapiens.UCSC.hg19 TxDb.Hsapiens.UCSC.hg19.knownGene Homo.sapiens SNPlocs.Hsapiens.dbSNP144.GRCh37 XtraSNPlocs.Hsapiens.dbSNP144.GRCh37 rsnps Biostrings MafDb.1Kgenomes.phase3.hs37d5 MafDb.ExAC.r1.0.hs37d5 MafDb.gnomADex.r2.1.hs37d5 COSMIC.67 rentrez PolyPhen.Hsapiens.dbSNP131 SIFT.Hsapiens.dbSNP137 seqinr openxlsx Rsamtools stringr utils stats GenomicRanges S4Vectors GenomicFeatures IRanges GenomicScores SummarizedExperiment xlsx: rJava xlsxjars grDevices utils dyebiasexamples: marray GEOquery ADGofTest: shinydashboardPlus: shiny htmltools shinydashboard fresh waiter lifecycle spsComps: shiny spsUtil assertthat stringr glue magrittr bsplus shinyFiles shinyWidgets shinytoastr shinyAce htmltools vroom dplyr utils R6 crayon gtable: grid CMplot: methyvimData: minfi energy: Rcpp stats boot gsl opencpu: evaluate httpuv knitr jsonlite remotes sys webutils curl rappdirs zip mime protolite brew openssl TMixClust: gss mvtnorm stats zoo cluster utils BiocParallel flexclust grDevices graphics Biobase SPEM qpgraph: methods parallel Matrix grid annotate graph Biobase S4Vectors BiocParallel AnnotationDbi IRanges GenomeInfoDb GenomicRanges GenomicFeatures mvtnorm qtl Rgraphviz operator.tools: utils LungCancerLines: Rsamtools NHPoisson: methods stats4 parallel car org.Mmu.eg.db: methods AnnotationDbi pROC: methods plyr Rcpp MSstatsQC: dplyr plotly ggplot2 ggExtra stats grid MSnbase qcmetrics GenomicTools.fileHandler: data.table snpStats frenchFISH: utils MCMCpack NHPoisson iBMQ: Biobase ggplot2 FGNet: igraph hwriter R.utils XML plotrix reshape2 RColorBrewer png methods stats utils graphics grDevices conquer: Rcpp Matrix matrixStats stats RcppArmadillo ggalt: ggplot2 utils graphics grDevices dplyr RColorBrewer KernSmooth proj4 scales grid gtable ash maps MASS extrafont tibble plotly assertive.types: assertive.base assertive.properties codetools methods stats metabCombiner: dplyr methods mgcv caret S4Vectors stats utils rlang graphics matrixStats lpSolve: DEWSeq: R.utils DESeq2 BiocParallel BiocGenerics data.table GenomeInfoDb GenomicRanges methods S4Vectors SummarizedExperiment stats utils GSVA: methods stats utils graphics BiocGenerics S4Vectors IRanges Biobase SummarizedExperiment GSEABase parallel BiocParallel SparseSignatures: NMF nnlasso nnls parallel data.table Biostrings GenomicRanges IRanges BSgenome GenomeInfoDb ggplot2 gridExtra reshape2 org.EcK12.eg.db: methods AnnotationDbi GeneticsPed: MASS gdata genetics forestplot: grid magrittr checkmate human610quadv1bCrlmm: utils structToolbox: struct ggplot2 ggthemes grid gridExtra methods scales sp stats utils testthat: brio callr cli crayon desc digest ellipsis evaluate jsonlite lifecycle magrittr methods pkgload praise processx ps R6 rlang utils waldo withr hgfocuscdf: utils AnnotationDbi latex2exp: stringr magrittr DDRTree: irlba Rcpp RcppEigen BH srnadiff: Rcpp methods devtools S4Vectors GenomeInfoDb rtracklayer SummarizedExperiment IRanges GenomicRanges DESeq2 Rsamtools GenomicFeatures GenomicAlignments grDevices Gviz BiocParallel BiocManager BiocStyle pRolocGUI: methods pRoloc Biobase MSnbase shiny scales dplyr DT graphics utils ggplot2 shinydashboardPlus colourpicker shinyhelper shinyWidgets shinyjs colorspace shinydashboard stats grDevices grid BiocGenerics traseR: GenomicRanges IRanges BSgenome.Hsapiens.UCSC.hg19 RANKS: methods graph RBGL limma NetPreProc PerfMeas ILoReg: Matrix parallel foreach aricode LiblineaR SparseM ggplot2 cowplot RSpectra umap Rtsne fastcluster parallelDist cluster dendextend DescTools plyr scales pheatmap reshape2 dplyr doRNG SingleCellExperiment SummarizedExperiment S4Vectors methods stats doSNOW utils curry: KEGGprofile: AnnotationDbi png TeachingDemos XML KEGG.db KEGGREST biomaRt RCurl ggplot2 reshape2 coRdon: methods stats utils Biostrings Biobase dplyr stringr purrr ggplot2 data.table brendaDb: dplyr Rcpp tibble stringr magrittr purrr BiocParallel crayon utils tidyr curl xml2 grDevices rlang BiocFileCache rappdirs hgu95av2cdf: utils AnnotationDbi CNORdt: CellNOptR abind gridBase: graphics grid R3CPET: Rcpp methods parallel ggplot2 pheatmap clValid igraph data.table reshape2 Hmisc RCurl BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges ggbio svMisc: utils methods stats tools inveRsion: methods haplo.stats graphics utils curl: cghMCR: methods DNAcopy CNTools limma BiocGenerics stats4 CLL: affy Biobase lfda: plyr grDevices rARPACK abind: methods utils memuse: methods utils HiveR: grid plyr jpeg png RColorBrewer utils stats rgl tcltk lfa: corpcor synapter: methods MSnbase RColorBrewer lattice qvalue multtest utils tools Biobase knitr Biostrings cleaver readr rmarkdown CMA: methods stats Biobase NoRCE: KEGGREST png dplyr graphics RSQLite DBI tidyr grDevices S4Vectors SummarizedExperiment reactome.db rWikiPathways RCurl dbplyr utils ggplot2 igraph stats reshape2 readr GO.db zlibbioc biomaRt rtracklayer IRanges GenomicRanges GenomicFeatures AnnotationDbi les: methods graphics fdrtool boot gplots RColorBrewer ChemoSpec: ChemoSpecUtils plyr stats utils grDevices readJDX desc: utils R6 crayon rprojroot ROCR: methods graphics grDevices gplots stats pathVar: methods ggplot2 gridExtra EMT mclust Matching data.table stats grDevices graphics utils zip: beadarraySNP: methods Biobase quantsmooth scAlign: SingleCellExperiment Seurat tensorflow purrr irlba Rtsne ggplot2 methods utils FNN edge: Biobase methods splines sva snm jackstraw qvalue MASS Matrix: methods graphics grid stats utils lattice tximportData: selectr: methods stringr R6 mbkmeans: methods DelayedArray Rcpp S4Vectors SingleCellExperiment SummarizedExperiment bluster ClusterR benchmarkme Matrix BiocParallel RcppArmadillo Rhdf5lib beachmat miRSM: WGCNA flashClust dynamicTreeCut GFA igraph linkcomm MCL NMF biclust iBBiG fabia BicARE isa2 s4vd BiBitR rqubic Biobase PMA stats dbscan subspace mclust SOMbrero ppclust miRspongeR Rcpp utils SummarizedExperiment GSEABase org.Hs.eg.db MatrixCorrelation energy mdgsa: AnnotationDbi DBI GO.db KEGG.db cluster Matrix WES.1KG.WUGSC: IlluminaHumanMethylationEPICmanifest: minfi enrichTF: pipeFrame BSgenome rtracklayer motifmatchr TFBSTools R.utils methods JASPAR2018 GenomeInfoDb GenomicRanges IRanges BiocGenerics S4Vectors utils parallel stats ggpubr heatmap3 ggplot2 clusterProfiler rmarkdown grDevices magrittr RJSONIO: methods sangeranalyseR: stringr ape Biostrings DECIPHER parallel reshape2 phangorn sangerseqR gridExtra shiny shinydashboard shinyjs data.table plotly DT zeallot excelR shinycssloaders ggdendro shinyWidgets openxlsx tools rmarkdown kableExtra seqinr BiocStyle logger shape: stats graphics grDevices metagenomeFeatures: Biobase Biostrings S4Vectors dplyr dbplyr stringr lazyeval RSQLite magrittr methods lattice ape DECIPHER vbmp: xml2: methods TFEA.ChIP: GenomicRanges IRanges biomaRt GenomicFeatures grDevices dplyr stats utils R.utils methods org.Hs.eg.db ASSIGN: gplots graphics grDevices msm Rlab stats sva utils ggplot2 yaml miRmine: SummarizedExperiment DEFormats: checkmate data.table DESeq2 edgeR GenomicRanges methods S4Vectors stats SummarizedExperiment genetics: combinat gdata gtools MASS mvtnorm netboost: Rcpp RcppParallel parallel grDevices graphics stats utils dynamicTreeCut WGCNA impute colorspace methods R.utils RBM: limma marray scBFA: SingleCellExperiment SummarizedExperiment Seurat MASS zinbwave stats copula ggplot2 DESeq2 utils grid methods Matrix levi: DT RColorBrewer colorspace dplyr ggplot2 httr igraph reshape2 shiny shinydashboard shinyjs xml2 knitr Rcpp grid grDevices stats utils testthat methods nucleoSim: stats IRanges S4Vectors graphics methods erma: methods Homo.sapiens GenomicFiles rtracklayer S4Vectors BiocGenerics GenomicRanges SummarizedExperiment ggplot2 GenomeInfoDb Biobase shiny BiocParallel IRanges AnnotationDbi htmlwidgets: grDevices htmltools jsonlite yaml RNAseqData.HNRNPC.bam.chr14: assertive: assertive.base assertive.properties assertive.types assertive.numbers assertive.strings assertive.datetimes assertive.files assertive.sets assertive.matrices assertive.models assertive.data assertive.data.uk assertive.data.us assertive.reflection assertive.code knitr pathprintGEOData: KEGGandMetacoreDzPathwaysGEO: Biobase BiocGenerics Polyfit: DESeq lhs: Rcpp SeqArray: gdsfmt methods parallel IRanges GenomicRanges GenomeInfoDb Biostrings S4Vectors categoryCompare: Biobase BiocGenerics AnnotationDbi hwriter GSEABase Category GOstats annotate colorspace graph RCy3 methods grDevices utils RCM: RColorBrewer alabama edgeR reshape2 tseries VGAM ggplot2 nleqslv phyloseq tensor MASS stats grDevices graphics methods tensorflow: config jsonlite processx reticulate tfruns utils yaml rstudioapi CPE: survival rms plyr: Rcpp binr: JASPAR2014: methods Biostrings curatedOvarianData: affy BiocGenerics subSeq: data.table dplyr tidyr ggplot2 magrittr qvalue digest Biobase ChIC.data: caret NPARC: dplyr tidyr BiocParallel broom MASS rlang magrittr stats methods JASPAR2016: methods BSgenome.Hsapiens.NCBI.GRCh38: BSgenome timeOmics: mixOmics dplyr tidyr tibble purrr magrittr ggplot2 stringr ggrepel propr lmtest knn.covertree: Rcpp RcppEigen Matrix methods shadowtext: ggplot2 grid scales JASPAR2018: methods Ckmeans.1d.dp: Rcpp Rdpack kza: EpiTxDb: AnnotationDbi Modstrings methods utils httr xml2 curl GenomicFeatures GenomicRanges GenomeInfoDb BiocGenerics BiocFileCache S4Vectors IRanges RSQLite DBI Biostrings tRNAdbImport ggseqlogo: ggplot2 data.table: methods factDesign: Biobase stats speedglm: Matrix MASS methods stats FastqCleaner: methods shiny stats IRanges Biostrings ShortRead DT S4Vectors graphics htmltools shinyBS Rcpp MIRA: BiocGenerics S4Vectors IRanges GenomicRanges data.table ggplot2 Biobase stats bsseq methods ribosomeProfilingQC: GenomicRanges AnnotationDbi BiocGenerics Biostrings BSgenome EDASeq GenomicAlignments GenomicFeatures GenomeInfoDb IRanges methods motifStack rtracklayer Rsamtools RUVSeq Rsubread S4Vectors XVector ggplot2 ggfittext scales ggrepel utils cluster stats graphics grid ViSEAGO: data.table AnnotationDbi AnnotationForge biomaRt dendextend DiagrammeR DT dynamicTreeCut fgsea GOSemSim ggplot2 GO.db grDevices heatmaply htmlwidgets igraph methods plotly processx topGO RColorBrewer R.utils scales stats UpSetR utils dynamicTreeCut: stats scMAGeCK: Seurat stats utils JASPAR2020: methods AgiMicroRna: methods Biobase limma affy preprocessCore affycoretools R.utils: R.oo methods utils tools R.methodsS3 FScanR: stats Imetagene: metagene shiny d3heatmap shinyBS shinyFiles shinythemes ggplot2 MADSEQ: rjags VGAM coda BSgenome BSgenome.Hsapiens.UCSC.hg19 S4Vectors methods preprocessCore GenomicAlignments Rsamtools Biostrings GenomicRanges IRanges VariantAnnotation SummarizedExperiment GenomeInfoDb rtracklayer graphics stats grDevices utils zlibbioc vcfR GeneAnswers: igraph RCurl annotate Biobase methods XML RSQLite MASS Heatplus RColorBrewer RBGL downloader edgeR: limma methods graphics stats utils locfit Rcpp chemometrics: rpart class e1071 MASS nnet pcaPP robustbase som lars pls mclust OmnipathR: igraph graphics methods utils jsonlite dplyr stats rlang tidyr hypergraph: methods utils graph rpart: graphics stats grDevices JADE: clue graphics assertive.code: assertive.base assertive.properties assertive.types methods gghighlight: ggplot2 dplyr ggrepel lifecycle purrr rlang tibble SpatialCPie: colorspace data.table digest dplyr ggforce ggiraph ggplot2 ggrepel grid igraph lpSolve methods purrr readr rlang shiny shinycssloaders shinyjs shinyWidgets stats SummarizedExperiment tibble tidyr tidyselect tools utils zeallot NISTunits: hgug4112a.db: methods AnnotationDbi org.Hs.eg.db utils: DBI: methods ggcyto: methods ggplot2 flowCore ncdfFlow flowWorkspace plyr scales hexbin data.table RColorBrewer gridExtra rlang ArrayTV: methods foreach S4Vectors IRanges DNAcopy oligoClasses pkgbuild: callr cli crayon desc prettyunits R6 rprojroot withr ASICS: BiocParallel ggplot2 glmnet grDevices gridExtra methods mvtnorm PepsNMR plyr quadprog ropls stats SummarizedExperiment utils Matrix zoo methylSig: bsseq DelayedArray DelayedMatrixStats DSS IRanges GenomeInfoDb GenomicRanges methods parallel stats S4Vectors widgetTools: methods utils tcltk selectKSigs: HiLDA magrittr gtools methods Rcpp clusterStab: Biobase methods PathNetData: remotes: methods stats tools utils conicfit: pracma geigen zoo: stats utils graphics grDevices lattice sctransform: MASS Matrix methods future.apply future ggplot2 reshape2 gridExtra matrixStats RcppArmadillo Rcpp ABSSeq: methods locfit limma praise: BUMHMM: devtools stringi gtools stats utils SummarizedExperiment Biostrings IRanges fitdistrplus: MASS grDevices survival methods stats garfield: batchtools: backports base64url brew checkmate data.table digest fs parallel progress R6 rappdirs stats stringi utils withr dualKS: Biobase affy methods graphics FlowRepositoryR: XML RCurl tools utils jsonlite limma: grDevices graphics stats utils methods mapproj: maps stats graphics catnet: methods stats utils graphics SVAPLSseq: methods stats SummarizedExperiment edgeR ggplot2 limma lmtest parallel pls pepXMLTab: XML vbsr: SingleCellSignalR: BiocManager circlize limma igraph gplots grDevices edgeR SIMLR data.table pheatmap stats Rtsne graphics stringr foreach multtest scran utils SpacePAC: iPAC oppar: Biobase methods GSEABase GSVA tseries: graphics stats utils quadprog zoo quantmod HTqPCR: Biobase RColorBrewer limma affy gplots graphics grDevices methods stats stats4 utils affycompData: methods Biobase affycomp BSgenome.Hsapiens.1000genomes.hs37d5: BSgenome psych: mnormt parallel stats graphics grDevices methods lattice nlme genArise: locfit tkrplot methods graphics grDevices stats tcltk utils xtable SNPRelate: gdsfmt methods ExperimentHub: methods BiocGenerics AnnotationHub BiocFileCache utils S4Vectors BiocManager curl rappdirs superheat: dplyr ggplot2 gtable magrittr plyr scales ggdendro vcfR: ape dplyr graphics grDevices magrittr memuse methods pinfsc50 Rcpp stats stringr tibble utils vegan viridisLite rbenchmark: CluMSIDdata: DeMixT: parallel Rcpp SummarizedExperiment knitr KernSmooth matrixcalc matrixStats stats truncdist base64enc ggplot2 DeMAND: KernSmooth methods RGraph2js: utils whisker rjson digest graph PSEA: Biobase MASS aCGH: cluster survival multtest Biobase grDevices graphics methods stats splines utils BiocOncoTK: methods utils ComplexHeatmap S4Vectors bigrquery shiny stats httr rjson dplyr magrittr grid DT GenomicRanges IRanges ggplot2 SummarizedExperiment DBI GenomicFeatures curatedTCGAData scales ggpubr plyr car graph Rgraphviz pingr: processx utils rsemmed: igraph methods magrittr stringr dplyr pqsfinder: Biostrings Rcpp GenomicRanges IRanges S4Vectors methods BH survivalsvm: survival pracma quadprog kernlab Matrix stats Hmisc HarmanData: MetaVolcanoR: methods data.table dplyr tidyr plotly ggplot2 cowplot parallel metafor metap rlang topconfects grDevices graphics stats htmlwidgets qvalue: splines ggplot2 grid reshape2 gridGraphics: grid graphics grDevices SNPhoodData: gaga: Biobase coda EBarrays mgcv simplifyEnrichment: BiocGenerics grid GOSemSim ComplexHeatmap circlize GetoptLong digest tm GO.db org.Hs.eg.db AnnotationDbi slam methods clue grDevices graphics stats utils proxyC Matrix cluster 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 CancerInSilico: Rcpp methods utils graphics stats BH TNBC.CMS: e1071 quadprog SummarizedExperiment GSVA pheatmap grDevices RColorBrewer pracma GGally R.utils forestplot ggplot2 ggpubr survival grid stats methods gage: graph KEGGREST AnnotationDbi GO.db mdqc: cluster MASS ReportingTools: methods knitr utils Biobase hwriter Category GOstats limma lattice AnnotationDbi edgeR annotate PFAM.db GSEABase BiocGenerics grid XML R.utils DESeq2 ggplot2 ggbio IRanges fBasics: timeDate timeSeries stats grDevices graphics methods utils MASS spatial gss stabledist EnsDb.Hsapiens.v75: ensembldb Risa: Biobase methods Rcpp biocViews affy xcms bnlearn: methods EnsDb.Hsapiens.v79: ensembldb oneSENSE: webshot shiny shinyFiles scatterplot3d Rtsne plotly gplots grDevices graphics stats utils methods flowCore loo: checkmate matrixStats parallel stats hgu133aprobe: AnnotationDbi nbconvertR: DFP: methods Biobase ResidualMatrix: methods Matrix S4Vectors DelayedArray SBMLR: XML deSolve PECA: ROTS limma affy genefilter preprocessCore aroma.affymetrix aroma.core branchpointer: caret plyr kernlab gbm stringr cowplot ggplot2 biomaRt Biostrings parallel utils stats BSgenome.Hsapiens.UCSC.hg38 rtracklayer GenomicRanges GenomeInfoDb IRanges S4Vectors data.table BAGS: breastCancerVDX Biobase AmpAffyExample: affy BUScorrect: gplots methods grDevices stats SummarizedExperiment pd.hugene.1.0.st.v1: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors chipenrich: AnnotationDbi BiocGenerics chipenrich.data GenomeInfoDb GenomicRanges grDevices grid IRanges lattice latticeExtra MASS methods mgcv org.Dm.eg.db org.Dr.eg.db org.Hs.eg.db org.Mm.eg.db org.Rn.eg.db parallel plyr rms rtracklayer S4Vectors stats stringr utils rScudo: methods stats igraph stringr grDevices Biobase S4Vectors SummarizedExperiment BiocGenerics rWikiPathways: httr utils XML rjson data.table tidyr RCurl googleCloudStorageR: assertthat curl googleAuthR httr jsonlite openssl utils yaml zip cummeRbund: BiocGenerics RSQLite ggplot2 reshape2 fastcluster rtracklayer Gviz methods plyr S4Vectors Biobase beadarrayExampleData: Biobase methods beadarray EnsDb.Hsapiens.v86: ensembldb pageRank: GenomicRanges igraph motifmatchr stats utils grDevices graphics gatingMLData: casper: Biobase IRanges methods GenomicRanges BiocGenerics coda EBarrays gaga gtools GenomeInfoDb GenomicFeatures limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM MsCoreUtils: methods S4Vectors MASS stats Rcpp Seurat: methods cluster cowplot fitdistrplus future future.apply ggplot2 ggrepel ggridges graphics grDevices grid httr ica igraph irlba jsonlite KernSmooth leiden lmtest MASS Matrix matrixStats miniUI patchwork pbapply plotly png RANN RColorBrewer Rcpp RcppAnnoy reticulate rlang ROCR Rtsne scales scattermore sctransform SeuratObject shiny spatstat.core spatstat.geom stats tibble tools utils uwot RcppEigen RcppProgress ggbio: methods BiocGenerics ggplot2 grid grDevices graphics stats utils gridExtra scales reshape2 gtable Hmisc biovizBase Biobase S4Vectors IRanges GenomeInfoDb GenomicRanges SummarizedExperiment Biostrings Rsamtools GenomicAlignments BSgenome VariantAnnotation rtracklayer GenomicFeatures OrganismDbi GGally ensembldb AnnotationDbi AnnotationFilter rlang gaia: CytoDx: doParallel dplyr glmnet rpart rpart.plot stats flowCore grDevices graphics utils snowfall: snow h5vcData: prettyunits: BEclear: BiocParallel futile.logger Rdpack Matrix data.table Rcpp outliers abind stats graphics utils methods exomeCopy: IRanges GenomicRanges Rsamtools stats4 methods GenomeInfoDb Fletcher2013a: limma Biobase VennDiagram gplots grid imager: magrittr Rcpp methods stringr png jpeg readbitmap grDevices purrr downloader igraph humanStemCell: Biobase hgu133plus2.db breastCancerNKI: Fletcher2013b: Fletcher2013a RTN RedeR igraph RColorBrewer plier: methods affy Biobase ChIPpeakAnno: methods IRanges GenomicRanges S4Vectors AnnotationDbi BiocGenerics Biostrings DBI dplyr ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures RBGL Rsamtools SummarizedExperiment VennDiagram biomaRt ggplot2 grDevices graph graphics grid KEGGREST matrixStats multtest regioneR rtracklayer stats utils phangorn: ape fastmatch graphics grDevices igraph magrittr Matrix methods parallel quadprog Rcpp stats utils segmentSeq: methods baySeq S4Vectors parallel GenomicRanges ShortRead stats Rsamtools IRanges GenomeInfoDb graphics grDevices utils abind famat: KEGGREST MPINet dplyr gprofiler2 rWikiPathways reactome.db stringr GO.db ontologyIndex tidyr shiny shinydashboard shinyBS plotly magrittr DT clusterProfiler org.Hs.eg.db covRNA: ade4 Biobase parallel genefilter grDevices stats graphics tmvnsim: ensurer: simpleCache: hierinf: fmsb glmnet methods parallel stats waveslim: graphics grDevices stats utils PCHiCdata: Chicago apComplex: graph RBGL Rgraphviz stats org.Sc.sgd.db metaseqR: EDASeq DESeq limma qvalue edgeR NOISeq baySeq NBPSeq biomaRt utils gplots corrplot vsn brew rjson log4r rvest: httr lifecycle magrittr rlang selectr tibble xml2 amplican: methods BiocGenerics Biostrings data.table Rcpp utils S4Vectors ShortRead IRanges GenomicRanges GenomeInfoDb BiocParallel gtable gridExtra ggplot2 ggthemes waffle stringr stats matrixStats Matrix dplyr rmarkdown knitr clusterCrit XtraSNPlocs.Hsapiens.dbSNP144.GRCh37: BSgenome methods utils BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges easyRNASeq: Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings DESeq edgeR GenomeInfoDb genomeIntervals GenomicAlignments GenomicRanges SummarizedExperiment graphics IRanges LSD locfit methods parallel rappdirs Rsamtools S4Vectors ShortRead utils XtraSNPlocs.Hsapiens.dbSNP144.GRCh38: BSgenome methods utils BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges geneplast: methods igraph snow ape grDevices graphics stats utils data.table biwt: rrcov MASS HDTD: stats Rcpp RcppArmadillo metagene2: R6 GenomicRanges BiocParallel rtracklayer tools GenomicAlignments GenomeInfoDb IRanges ggplot2 Rsamtools purrr data.table methods dplyr magrittr reshape2 dyebias: marray Biobase twoddpcr: class ggplot2 hexbin methods scales shiny stats utils RColorBrewer S4Vectors tibble: ellipsis fansi lifecycle magrittr methods pillar pkgconfig rlang utils vctrs GUIDEseq: GenomicRanges BiocGenerics BiocParallel Biostrings CRISPRseek ChIPpeakAnno data.table matrixStats BSgenome parallel IRanges S4Vectors GenomicAlignments GenomeInfoDb Rsamtools hash limma dplyr mimager: Biobase BiocGenerics S4Vectors preprocessCore grDevices methods grid gtable scales DBI affy affyPLM oligo oligoClasses MassSpecWavelet: waveslim lsa: SnowballC qckitfastq: magrittr ggplot2 dplyr seqTools zlibbioc data.table reshape2 grDevices graphics stats utils Rcpp rlang RSeqAn mouse4302cdf: utils AnnotationDbi scCB2: SingleCellExperiment SummarizedExperiment Matrix methods utils stats edgeR rhdf5 parallel DropletUtils doParallel iterators foreach Seurat pcxnData: beeswarm: stats graphics grDevices utils drosgenome1.db: methods AnnotationDbi org.Dm.eg.db InTAD: methods S4Vectors IRanges GenomicRanges MultiAssayExperiment SummarizedExperiment stats BiocGenerics Biobase rtracklayer parallel graphics mclust qvalue ggplot2 utils ggpubr OncoSimulR: Rcpp parallel data.table graph Rgraphviz gtools igraph methods RColorBrewer grDevices car dplyr smatr ggplot2 ggrepel MethReg: dplyr plyr GenomicRanges SummarizedExperiment DelayedArray ggplot2 ggpubr tibble tidyr S4Vectors sesameData stringr readr methods stats Matrix MASS rlang pscl IRanges sfsmisc progress callr: processx R6 utils broom.mixed: broom dplyr tidyr plyr purrr tibble reshape2 nlme methods stringr coda TMB cubelyr proDA: stats utils methods BiocGenerics SummarizedExperiment S4Vectors extraDistr openxlsx: grDevices methods Rcpp stats utils zip stringi assertive.data: assertive.base assertive.strings mco: robCompositions: ggplot2 pls data.table car cvTools e1071 fda rrcov cluster fpc GGally kernlab MASS mclust sROC tidyr robustbase splines VIM zCompositions reshape2 Rcpp RcppEigen minet: infotheo GenomicTools: gMWT Rcpp data.table GenomicTools.fileHandler circlize stringr snpStats RcppArmadillo hom.Rn.inp.db: methods AnnotationDbi BSgenome.Scerevisiae.UCSC.sacCer1: BSgenome MSstatsPTM: broom dplyr rlang stats tibble tidyr tidyselect Biostrings BSgenome.Scerevisiae.UCSC.sacCer2: BSgenome GateFinder: splancs mvoutlier methods stats diptest flowCore flowFP lsr: BSgenome.Scerevisiae.UCSC.sacCer3: BSgenome mefa: methods minfi: methods BiocGenerics GenomicRanges SummarizedExperiment Biostrings bumphunter S4Vectors GenomeInfoDb Biobase IRanges beanplot RColorBrewer lattice nor1mix siggenes limma preprocessCore illuminaio DelayedMatrixStats mclust genefilter nlme reshape MASS quadprog data.table GEOquery stats grDevices graphics utils DelayedArray HDF5Array BiocParallel RcppHNSW: methods Rcpp RGSEA: BiocGenerics irlba: Matrix stats methods easyreporting: rmarkdown methods tools varhandle: utils graphics ROC: utils methods knitr BSgenome.Ggallus.UCSC.galGal3: BSgenome discretecdAlgorithm: Rcpp sparsebnUtils igraph RcppEigen RANN: CircStats: MASS boot RcppEigen: Matrix Rcpp stats utils Chicago: data.table matrixStats MASS Hmisc Delaporte methods grDevices graphics stats utils foreach: codetools utils iterators mdp: ggplot2 gridExtra grid stats utils hom.Sc.inp.db: methods AnnotationDbi golubEsets: Biobase MANOR: GLAD graphics grDevices stats utils wavethresh: MASS splines2: Rcpp stats RcppArmadillo BSgenome.Ecoli.NCBI.20080805: BSgenome iCNV: CODEX fields ggplot2 truncnorm tidyr data.table dplyr grDevices graphics stats utils rlang shinydashboard: utils shiny htmltools promises RPA: affy BiocGenerics methods phyloseq janeaustenr: clipper: Matrix graph methods Biobase Rcpp igraph gRbase qpgraph KEGGgraph corpcor RBGL showimage: png tools ENmix: parallel doParallel foreach SummarizedExperiment stats grDevices graphics preprocessCore matrixStats methods utils irr geneplotter impute minfi RPMM illuminaio dynamicTreeCut IRanges gtools Biobase ExperimentHub AnnotationHub genefilter gplots quadprog S4Vectors oligo: BiocGenerics oligoClasses Biobase Biostrings affyio affxparser DBI ff graphics methods preprocessCore RSQLite splines stats stats4 utils zlibbioc coGPS: graphics grDevices km.ci: survival stats Rattus.norvegicus: AnnotationDbi methods OrganismDbi GenomicFeatures GO.db org.Rn.eg.db TxDb.Rnorvegicus.UCSC.rn5.refGene OMICsPCA: OMICsPCAdata HelloRanges fpc stats MultiAssayExperiment pdftools methods grDevices utils clValid NbClust cowplot rmarkdown kableExtra rtracklayer IRanges GenomeInfoDb reshape2 ggplot2 factoextra rgl corrplot MASS graphics FactoMineR PerformanceAnalytics tidyr data.table cluster magick mfa: methods stats ggplot2 Rcpp dplyr ggmcmc MCMCpack MCMCglmm coda magrittr tibble Biobase rebus.base: stats eegc: R.utils gplots sna wordcloud igraph pheatmap edgeR DESeq2 clusterProfiler S4Vectors ggplot2 org.Hs.eg.db org.Mm.eg.db limma DOSE AnnotationDbi RiboProfiling: Biostrings BiocGenerics GenomeInfoDb GenomicRanges IRanges reshape2 GenomicFeatures grid plyr S4Vectors GenomicAlignments ggplot2 ggbio Rsamtools rtracklayer data.table sqldf miRNAmeConverter: miRBaseVersions.db DBI AnnotationDbi reshape2 ANCOMBC: stats MASS nloptr Rdpack phyloseq microbiome staRank: methods cellHTS2 CellMapperData: ExperimentHub CellMapper messina: survival methods Rcpp plyr ggplot2 grid foreach graphics TransView: methods GenomicRanges BiocGenerics S4Vectors IRanges zlibbioc gplots Rhtslib PepsNMR: Matrix ptw ggplot2 gridExtra matrixStats reshape2 methods graphics stats rmdformats: knitr rmarkdown bookdown htmltools CytoML: cytolib flowCore flowWorkspace openCyto XML data.table jsonlite RBGL Rgraphviz Biobase methods graph graphics utils base64enc plyr dplyr grDevices ggcyto yaml lattice stats corpcor RUnit tibble RcppParallel xml2 Rcpp BH RProtoBufLib Rhdf5lib RcppArmadillo ROTS: Rcpp stats Biobase methods stringdist: parallel flowCore: Biobase BiocGenerics grDevices graphics methods stats utils stats4 Rcpp matrixStats cytolib S4Vectors RcppArmadillo BH RProtoBufLib multcompView: grid DeepBlueR: XML RCurl GenomicRanges data.table stringr diffr dplyr methods rjson utils R.utils foreach withr rtracklayer GenomeInfoDb settings filehash copynumber: BiocGenerics S4Vectors IRanges GenomicRanges SC3: graphics stats utils methods e1071 parallel foreach doParallel doRNG shiny ggplot2 pheatmap ROCR robustbase rrcov cluster WriteXLS Rcpp SummarizedExperiment SingleCellExperiment BiocGenerics S4Vectors RcppArmadillo omicRexposome: Biobase stats utils grDevices graphics methods rexposome limma sva ggplot2 ggrepel PMA omicade4 gridExtra MultiDataSet SmartSVA isva parallel SummarizedExperiment stringr OmicCircos: methods GenomicRanges GRENITS: Rcpp RcppArmadillo ggplot2 graphics grDevices reshape2 stats utils clippda: limma statmod rgl lattice scatterplot3d graphics grDevices stats utils Biobase tools methods MafDb.1Kgenomes.phase3.GRCh38: GenomicScores utils S4Vectors IRanges GenomicRanges GenomeInfoDb BSgenome nuCpos: graphics methods GenomicInteractions: InteractionSet Rsamtools rtracklayer GenomicRanges IRanges BiocGenerics data.table stringr GenomeInfoDb ggplot2 grid gridExtra methods igraph S4Vectors dplyr Gviz Biobase graphics stats utils grDevices ChIPanalyser: GenomicRanges Biostrings BSgenome RcppRoll parallel methods IRanges S4Vectors grDevices graphics stats utils rtracklayer ROCR BiocManager GenomeInfoDb ELMER.data: GenomicRanges altcdfenvs: methods BiocGenerics S4Vectors Biobase affy makecdfenv Biostrings hypergraph MethCP: methods utils stats S4Vectors bsseq DSS methylKit DNAcopy GenomicRanges IRanges GenomeInfoDb BiocParallel a4Reporting: methods xtable tokenizers: stringi Rcpp SnowballC concaveman: V8 sf magrittr jsonlite dplyr whisker: TarSeqQC: methods GenomicRanges Rsamtools ggplot2 plyr openxlsx grDevices stats utils S4Vectors IRanges BiocGenerics reshape2 GenomeInfoDb BiocParallel Biostrings cowplot graphics GenomicAlignments Hmisc ggridges: ggplot2 grid plyr scales withr PWMEnrich.Hsapiens.background: methods PWMEnrich filelock: ClusterSignificance: methods pracma princurve scatterplot3d RColorBrewer grDevices graphics utils stats betareg: graphics grDevices methods stats flexmix Formula lmtest modeltools sandwich strucchange: zoo sandwich graphics stats utils miRBaseConverter: stats CNEr: Biostrings DBI RSQLite GenomeInfoDb GenomicRanges rtracklayer XVector GenomicAlignments methods S4Vectors IRanges readr BiocGenerics tools parallel reshape2 ggplot2 poweRlaw annotate GO.db R.utils KEGGREST BicARE: Biobase multtest GSEABase maPredictDSC: MASS affy limma gcrma ROC class e1071 caret hgu133plus2.db ROCR AnnotationDbi LungCancerACvsSCCGEO mvtnorm: stats methods PGSEA: GO.db KEGG.db AnnotationDbi annaffy methods Biobase RbcBook1: Biobase graph rpart ACME: Biobase methods BiocGenerics graphics stats DOT: V8 tools clonotypeR: methods MMDiff2: Rsamtools Biobase GenomicRanges locfit BSgenome Biostrings shiny ggplot2 RColorBrewer graphics grDevices parallel S4Vectors methods GeneMeta: methods Biobase genefilter GenomeInfoDbData: BSgenome.Athaliana.TAIR.TAIR9: BSgenome survival: graphics Matrix methods splines stats utils TxDb.Mmusculus.UCSC.mm9.knownGene: GenomicFeatures AnnotationDbi methods: utils stats RIPAT: biomaRt GenomicRanges ggplot2 grDevices IRanges karyoploteR openxlsx plyr regioneR rtracklayer stats stringr utils RTN: methods RedeR minet viper mixtools snow stats limma data.table IRanges igraph S4Vectors SummarizedExperiment car pwr pheatmap grDevices graphics utils GEOquery: methods Biobase httr readr xml2 dplyr tidyr magrittr limma SimBindProfiles: methods Ringo limma mclust Biobase qsmooth: SummarizedExperiment utils sva stats methods graphics smoothie: makecdfenv: affyio Biobase affy methods stats utils zlibbioc hgu95acdf: utils AnnotationDbi colonCA: Biobase rlist: yaml jsonlite XML data.table fastmap: EBarrays: Biobase lattice methods cluster graphics grDevices stats SubCellBarCode: Rtsne scatterplot3d caret e1071 ggplot2 gridExtra networkD3 ggrepel graphics stats org.Hs.eg.db AnnotationDbi SNPlocs.Hsapiens.dbSNP.20120608: IRanges GenomicRanges BSgenome methods utils intervals: utils graphics methods basecallQC: stats utils methods rmarkdown knitr prettydoc yaml ggplot2 stringr XML raster dplyr data.table tidyr magrittr DT lazyeval ShortRead flowViz: flowCore lattice stats4 Biobase graphics grDevices grid KernSmooth latticeExtra MASS methods RColorBrewer stats utils hexbin IDPmisc smoother: TTR HELP: stats graphics grDevices Biobase methods gitcreds: jsonlite: methods SeqGate: S4Vectors SummarizedExperiment GenomicRanges stats methods BiocManager YAPSA: GenomicRanges ggplot2 grid limSolve SomaticSignatures VariantAnnotation GenomeInfoDb reshape2 gridExtra corrplot dendextend GetoptLong circlize gtrellis doParallel PMCMR ggbeeswarm ComplexHeatmap KEGGREST grDevices Biostrings BSgenome.Hsapiens.UCSC.hg19 magrittr pracma dplyr utils bc3net: c3net infotheo igraph Matrix lattice MesKit: methods data.table Biostrings dplyr tidyr ape ggrepel pracma ggridges AnnotationDbi IRanges circlize cowplot mclust phangorn ComplexHeatmap ggplot2 RColorBrewer grDevices stats utils S4Vectors lumi: Biobase affy methylumi GenomicFeatures GenomicRanges annotate lattice mgcv nleqslv KernSmooth preprocessCore RSQLite DBI AnnotationDbi MASS graphics stats stats4 methods Organism.dplyr: dplyr AnnotationFilter RSQLite S4Vectors GenomeInfoDb IRanges GenomicRanges GenomicFeatures AnnotationDbi rlang methods tools utils BiocFileCache DBI dbplyr tibble Basic4Cseq: Biostrings GenomicAlignments caTools GenomicRanges grDevices graphics stats utils methods RCircos BSgenome.Ecoli.NCBI.20080805 ReadqPCR: Biobase methods MafDb.ExAC.r1.0.hs37d5: GenomicScores utils S4Vectors IRanges GenomicRanges GenomeInfoDb BSgenome gsmoothr: methods Rtsne: Rcpp stats ChAMP: minfi ChAMPdata DMRcate Illumina450ProbeVariants.db IlluminaHumanMethylationEPICmanifest DT RPMM prettydoc Hmisc globaltest sva illuminaio rmarkdown IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno.ilm10b4.hg19 limma DNAcopy preprocessCore impute marray wateRmelon plyr goseq missMethyl kpmt ggplot2 GenomicRanges qvalue isva doParallel bumphunter quadprog shiny shinythemes plotly RColorBrewer dendextend matrixStats combinat Icens: survival graphics motifbreakR: grid MotifDb methods compiler grDevices grImport stringr BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges Biostrings BSgenome rtracklayer VariantAnnotation BiocParallel motifStack Gviz matrixStats TFMPvalue SummarizedExperiment findpython: lefser: SummarizedExperiment coin MASS ggplot2 stats methods bambu: SummarizedExperiment S4Vectors IRanges BiocGenerics BiocParallel data.table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges stats glmnet Rsamtools methods Rcpp RcppArmadillo CNVrd2: methods VariantAnnotation parallel rjags ggplot2 gridExtra DNAcopy IRanges Rsamtools nearBynding: R.utils matrixStats plyranges transport Rsamtools S4Vectors grDevices graphics rtracklayer dplyr GenomeInfoDb methods GenomicRanges utils stats magrittr TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene ggplot2 gplots BiocGenerics rlang RVS: GENLIB gRain snpStats kinship2 methods stats utils MetaNeighbor: grDevices graphics methods stats utils Matrix matrixStats beanplot gplots RColorBrewer SummarizedExperiment SingleCellExperiment igraph dplyr tidyr tibble ggplot2 intrinsicDimension: yaImpute miniUI: shiny htmltools utils utf8: lumiHumanAll.db: methods AnnotationDbi org.Hs.eg.db SpatialExperiment: methods SingleCellExperiment S4Vectors objectProperties: methods objectSignals EDASeq: Biobase ShortRead methods graphics BiocGenerics IRanges aroma.light Rsamtools biomaRt Biostrings AnnotationDbi GenomicFeatures GenomicRanges BiocManager TxDb.Celegans.UCSC.ce11.refGene: GenomicFeatures AnnotationDbi KCsmart: siggenes multtest KernSmooth methods BiocGenerics mlr: ParamHelpers backports BBmisc checkmate data.table ggplot2 methods parallelMap stats stringi survival utils XML lungExpression: Biobase DTA: LSD scatterplot3d DSS: methods Biobase BiocParallel bsseq utils graphics stats splines DelayedArray geneAttribution: utils GenomicRanges org.Hs.eg.db BiocGenerics GenomeInfoDb GenomicFeatures IRanges rtracklayer RBGL: graph methods BH ADAM: stats utils methods Rcpp GO.db KEGGREST knitr pbapply dplyr DT stringr SummarizedExperiment affycomp: methods Biobase recipes: dplyr ellipsis generics glue gower ipred lifecycle lubridate magrittr Matrix purrr rlang stats tibble tidyr tidyselect timeDate utils withr grImport: methods grDevices graphics grid XML SBGNview: pathview SBGNview.data Rdpack grDevices methods stats utils xml2 rsvg igraph rmarkdown knitr SummarizedExperiment AnnotationDbi httr KEGGREST bookdown HilbertVis: grid lattice ternarynet: methods utils igraph shinytoastr: shiny RcisTarget.hg19.motifDBs.cisbpOnly.500bp: data.table MethylSeekR: rtracklayer parallel mhsmm IRanges BSgenome GenomicRanges geneplotter graphics grDevices stats utils ROCit: stats graphics utils methods humanCHRLOC: CEMiTool: methods scales dplyr data.table WGCNA grid ggplot2 ggpmisc ggthemes ggrepel sna clusterProfiler fgsea stringr knitr rmarkdown igraph DT htmltools pracma intergraph grDevices utils network matrixStats ggdendro gridExtra gtable fastcluster yeast2.db: methods AnnotationDbi org.Sc.sgd.db viper: Biobase methods mixtools stats parallel e1071 KernSmooth GAprediction: glmnet stats utils Matrix ChromSCape: shiny colourpicker shinyjs rtracklayer shinyFiles shinyhelper shinycssloaders Matrix plotly shinydashboard colorRamps kableExtra viridis batchelor BiocParallel parallel Rsamtools ggplot2 qualV stringdist fs DT scran scater ConsensusClusterPlus Rtsne dplyr tidyr GenomicRanges IRanges irlba rlist umap tibble methods jsonlite edgeR stats graphics grDevices utils S4Vectors SingleCellExperiment SummarizedExperiment msigdbr DEqMS: graphics stats ggplot2 limma minqa: Rcpp dearseq: CompQuadForm ggplot2 KernSmooth matrixStats methods parallel pbapply stats statmod RMassBankData: biocGraph: Rgraphviz graph geneplotter BiocGenerics methods timeSeries: graphics grDevices stats methods utils timeDate log4r: itertools: iterators parallel ToxicoGx: CoreGx SummarizedExperiment S4Vectors Biobase BiocParallel ggplot2 tibble dplyr caTools downloader magrittr methods reshape2 tidyr data.table assertthat scales graphics grDevices parallel stats utils limma SIM: quantreg graphics stats globaltest quantsmooth ShortRead: BiocGenerics BiocParallel Biostrings Rsamtools GenomicAlignments Biobase S4Vectors IRanges GenomeInfoDb GenomicRanges hwriter methods zlibbioc lattice latticeExtra XVector Rhtslib RPMG: normr: methods stats utils grDevices parallel GenomeInfoDb GenomicRanges IRanges Rcpp qvalue bamsignals rtracklayer gwascat: methods S4Vectors IRanges GenomeInfoDb GenomicRanges GenomicFeatures readr Biostrings AnnotationDbi BiocFileCache snpStats VariantAnnotation HPAanalyze: dplyr openxlsx ggplot2 tibble xml2 stats utils gridExtra Clomial: matrixStats methods permute msmsEDA: MSnbase MASS gplots RColorBrewer akima: sp IlluminaDataTestFiles: RPMM: cluster scDataviz: S4Vectors SingleCellExperiment ggplot2 ggrepel flowCore umap Seurat reshape2 scales RColorBrewer corrplot stats grDevices graphics utils MASS matrixStats methods cubelyr: dplyr glue pillar purrr rlang tibble tidyselect corrgram: graphics grDevices stats DESeq: BiocGenerics Biobase locfit lattice genefilter geneplotter methods MASS RColorBrewer TargetScore: pracma Matrix oppti: limma stats reshape ggplot2 grDevices RColorBrewer pheatmap knitr methods devtools amap: OCplus: multtest graphics grDevices stats akima BiRewire: igraph slam tsne Matrix proFIA: xcms stats graphics utils grDevices methods pracma Biobase minpack.lm BiocParallel missForest ropls SuppDists: bionetdata: RnaSeqSampleSize: RnaSeqSampleSizeData biomaRt edgeR heatmap3 matlab KEGGREST methods grDevices graphics stats utils Rcpp cpvSNP: GenomicFeatures GSEABase methods corpcor BiocParallel ggplot2 plyr dtplyr: crayon data.table dplyr ellipsis glue lifecycle rlang tibble tidyselect vctrs PCpheno: Category ScISI SLGI ppiStats ppiData annotate AnnotationDbi Biobase GO.db graph graphics GSEABase KEGG.db methods stats stats4 goSTAG: AnnotationDbi biomaRt GO.db graphics memoise stats utils RUVnormalizeData: Biobase clValid: cluster methods class hugene10sttranscriptcluster.db: methods AnnotationDbi org.Hs.eg.db basilisk.utils: utils methods rappdirs filelock DEXSeq: BiocParallel Biobase SummarizedExperiment IRanges GenomicRanges DESeq2 AnnotationDbi RColorBrewer S4Vectors BiocGenerics biomaRt hwriter methods stringr Rsamtools statmod geneplotter genefilter twilight: splines stats Biobase graphics grDevices heatmaply: plotly viridis ggplot2 dendextend magrittr reshape2 scales seriation utils stats grDevices methods colorspace RColorBrewer htmlwidgets webshot assertthat egg diffusr: Rcpp igraph methods RcppEigen mpm: MASS KernSmooth rpart.plot: rpart Rfast: Rcpp RcppZiggurat RcppArmadillo Doscheda: methods drc stats httr jsonlite reshape2 vsn affy limma stringr ggplot2 graphics grDevices calibrate corrgram gridExtra DT shiny shinydashboard readxl prodlim matrixStats pdist: methods girafe: methods BiocGenerics S4Vectors Rsamtools intervals ShortRead genomeIntervals grid Biobase Biostrings graphics grDevices stats utils IRanges iCARE: plotrix gtools Hmisc quantro: Biobase minfi doParallel foreach iterators ggplot2 methods RColorBrewer moments: metR: checkmate data.table digest fields Formula formula.tools ggplot2 grid gtable lubridate memoise plyr scales sp stringr purrr RCurl isoband MSstatsConvert: data.table log4r methods checkmate utils ExiMiR: Biobase affy limma affyio preprocessCore gpls: stats ipdDb: methods AnnotationDbi AnnotationHub Biostrings GenomicRanges RSQLite DBI IRanges stats assertthat ITALICS: GLAD ITALICSData oligo affxparser pd.mapping50k.xba240 DBI oligoClasses stats Rttf2pt1: MiChip: Biobase TCGAbiolinks: downloader grDevices biomaRt dplyr graphics tibble GenomicRanges XML data.table jsonlite plyr knitr methods ggplot2 stringr IRanges rvest stats utils S4Vectors R.utils SummarizedExperiment TCGAbiolinksGUI.data readr tools tidyr purrr xml2 httr rdetools: FitHiC: data.table fdrtool grDevices graphics Rcpp stats utils triplex: S4Vectors IRanges XVector Biostrings methods grid GenomicRanges BSgenome.Hsapiens.UCSC.hg38.masked: BSgenome BSgenome.Hsapiens.UCSC.hg38 phenopath: Rcpp SummarizedExperiment methods stats dplyr tibble ggplot2 tidyr orQA: Rcpp gtools genefilter nlme GGPA: stats methods graphics GGally network sna scales matrixStats Rcpp RcppArmadillo Cormotif: affy limma graphics grDevices geneLenDataBase: utils rtracklayer GenomicFeatures Dune: BiocParallel SummarizedExperiment mclust utils ggplot2 dplyr tidyr RColorBrewer magrittr gganimate purrr multiOmicsViz: methods parallel doParallel foreach grDevices graphics utils SummarizedExperiment stats Homo.sapiens: AnnotationDbi methods OrganismDbi GenomicFeatures GO.db org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene GNET2: ggplot2 xgboost Rcpp reshape2 grid DiagrammeR methods stats matrixStats graphics SummarizedExperiment dplyr igraph grDevices utils pd.mapping50k.xba240: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors spkTools: Biobase graphics grDevices gtools methods RColorBrewer stats utils robustbase: stats graphics utils methods DEoptimR scRecover: stats utils methods graphics doParallel foreach parallel penalized kernlab rsvd Matrix MASS pscl bbmle gamlss preseqR SAVER Rmagic BiocParallel msa: methods Biostrings Rcpp BiocGenerics IRanges S4Vectors tools iterClust: Biobase cluster stats methods formatR: miRspongeR: corpcor parallel igraph MCL clusterProfiler ReactomePA DOSE survival grDevices graphics stats varhandle linkcomm utils Rcpp org.Hs.eg.db pkgDepTools: methods graph RBGL cellHTS2: RColorBrewer Biobase methods genefilter splots vsn hwriter locfit grid prada GSEABase Category stats4 BiocGenerics profileScoreDist: Rcpp BiocGenerics methods graphics gQTLstats: Homo.sapiens methods snpStats BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicFiles GenomicRanges SummarizedExperiment VariantAnnotation Biobase BatchJobs gQTLBase limma mgcv dplyr AnnotationDbi GenomicFeatures ggplot2 reshape2 doParallel foreach ffbase BBmisc beeswarm HardyWeinberg graphics stats utils shiny plotly erma ggbeeswarm msm: survival mvtnorm expm PPInfer: biomaRt fgsea kernlab ggplot2 igraph STRINGdb yeastExpData ontologyIndex: GlobalAncova: methods corpcor globaltest annotate AnnotationDbi Biobase dendextend GSEABase VGAM OGSA: gplots limma Biobase Onassis: rJava OnassisJavaLibs GEOmetadb RSQLite data.table methods tools utils AnnotationDbi RCurl stats DT knitr Rtsne dendextend clusteval ggplot2 ggfortify TxDb.Celegans.UCSC.ce11.ensGene: GenomicFeatures AnnotationDbi motifmatchr: Matrix Rcpp methods TFBSTools Biostrings BSgenome S4Vectors SummarizedExperiment GenomicRanges IRanges Rsamtools GenomeInfoDb RcppArmadillo illuminaio: base64 knitrBootstrap: knitr rmarkdown markdown GGdata: methods Biobase GGBase snpStats illuminaHumanv1.db AnnotationDbi RedeR: methods igraph COCOA: GenomicRanges BiocGenerics S4Vectors IRanges data.table ggplot2 Biobase stats methods ComplexHeatmap MIRA tidyr grid grDevices simpleCache fitdistrplus methInheritSim: methylKit GenomicRanges GenomeInfoDb parallel BiocGenerics S4Vectors methods stats IRanges msm MatrixGenerics: matrixStats methods TFHAZ: GenomicRanges S4Vectors grDevices graphics stats utils IRanges methods AUCell: data.table graphics grDevices GSEABase methods mixtools R.utils shiny stats SummarizedExperiment BiocGenerics S4Vectors utils XVector: methods BiocGenerics S4Vectors IRanges utils tools zlibbioc splatter: SingleCellExperiment BiocGenerics BiocParallel checkmate edgeR fitdistrplus ggplot2 locfit matrixStats methods scales scater stats SummarizedExperiment utils crayon S4Vectors grDevices hdrcde: locfit ash ks KernSmooth ggplot2 RColorBrewer benchmarkme: benchmarkmeData compiler doParallel dplyr foreach graphics httr Matrix methods parallel tibble utils BatchJobs: BBmisc methods backports brew checkmate data.table DBI digest parallel RSQLite sendmailR stats stringi utils ecolicdf: utils AnnotationDbi frma: Biobase MASS DBI affy methods oligo oligoClasses preprocessCore utils BiocGenerics Rmmquant: Rcpp methods S4Vectors GenomicRanges SummarizedExperiment devtools TBX20BamSubset TxDb.Mmusculus.UCSC.mm9.knownGene org.Mm.eg.db DESeq2 BiocStyle gemini: dplyr grDevices ggplot2 magrittr mixtools scales pbmcapply parallel stats utils lintr: rex crayon codetools cyclocomp testthat digest rstudioapi httr jsonlite knitr stats utils xml2 xmlparsedata emmeans: estimability graphics methods numDeriv stats utils plyr mvtnorm xtable EnhancedVolcano: ggplot2 ggrepel ggalt ggrastr shinyFiles: htmltools jsonlite tools shiny fs tibble gpart: grid Homo.sapiens TxDb.Hsapiens.UCSC.hg38.knownGene igraph biomaRt Rcpp data.table OrganismDbi AnnotationDbi grDevices stats utils GenomicRanges IRanges SCANVIS: IRanges plotrix RCurl rtracklayer GOsummaries: Rcpp plyr grid gProfileR reshape2 limma ggplot2 gtable h5vc: grid gridExtra ggplot2 rhdf5 reshape S4Vectors IRanges Biostrings Rsamtools methods GenomicRanges abind BiocParallel BatchJobs h5vcData GenomeInfoDb Rhtslib PairedData: methods graphics MASS gld mvtnorm lattice ggplot2 GeneGA: seqinr hash methods Rtreemix: methods graph Biobase Hmisc seriation: stats grDevices grid TSP qap cluster gclus dendextend colorspace MASS gplots registry SingleR: SummarizedExperiment methods Matrix S4Vectors DelayedArray DelayedMatrixStats BiocNeighbors BiocParallel BiocSingular stats utils Rcpp beachmat statmod: stats graphics LungCancerACvsSCCGEO: extRemes: Lmoments distillery graphics stats pd.mapping250k.nsp: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors ALDEx2: methods stats zCompositions BiocParallel GenomicRanges IRanges S4Vectors SummarizedExperiment multtest parallelDist: Rcpp RcppParallel RcppArmadillo MetCirc: amap circlize scales shiny MSnbase ggplot2 S4Vectors miRNATarget: Biobase rcellminerData: Biobase httpcode: mosaics: methods graphics Rcpp MASS splines lattice IRanges GenomicRanges GenomicAlignments Rsamtools GenomeInfoDb S4Vectors OncoScore: biomaRt grDevices graphics utils methods Roleswitch: pracma reshape plotrix microRNA biomaRt Biostrings Biobase DBI spicyR: ggplot2 concaveman BiocParallel spatstat.core spatstat.geom lmerTest BiocGenerics S4Vectors lme4 methods mgcv pheatmap rlang grDevices IRanges stats data.table dplyr tidyr Mirsynergy: igraph ggplot2 graphics grDevices gridExtra Matrix parallel RColorBrewer reshape scales utils deldir: graphics grDevices bioassayR: DBI RSQLite methods Matrix rjson BiocGenerics XML ChemmineR RNAAgeCalc: ggplot2 recount impute AnnotationDbi org.Hs.eg.db stats SummarizedExperiment methods MEDIPSData: SMVar: SQN: mclust nor1mix QFeatures: MultiAssayExperiment methods stats utils S4Vectors IRanges SummarizedExperiment BiocGenerics ProtGenerics AnnotationFilter lazyeval Biobase MsCoreUtils EMT: CausalR: igraph yeastRNASeq: BSgenome.Btaurus.UCSC.bosTau6: BSgenome iSEE: SummarizedExperiment SingleCellExperiment methods BiocGenerics S4Vectors utils stats shiny shinydashboard shinyAce shinyjs DT rintrojs ggplot2 ggrepel colourpicker igraph vipor mgcv graphics grDevices viridisLite shinyWidgets ComplexHeatmap circlize grid shinyTANDEM: rTANDEM shiny mixtools methods xtable MeSH.Cel.eg.db: MeSHDbi multicool: methods Rcpp RCAS: plotly DT data.table GenomicRanges IRanges BSgenome BSgenome.Hsapiens.UCSC.hg19 GenomeInfoDb Biostrings rtracklayer GenomicFeatures rmarkdown genomation knitr BiocGenerics S4Vectors plotrix pbapply RSQLite proxy pheatmap ggplot2 cowplot ggseqlogo utils ranger gprofiler2 xtable: stats utils oligoData: oligo UniProt.ws: methods utils RSQLite RCurl BiocGenerics AnnotationDbi BiocFileCache rappdirs geneplotter: methods Biobase BiocGenerics lattice annotate AnnotationDbi graphics grDevices grid RColorBrewer stats utils BiocSingular: BiocGenerics S4Vectors Matrix methods utils DelayedArray BiocParallel irlba rsvd Rcpp beachmat GenomicRanges: methods stats4 BiocGenerics S4Vectors IRanges GenomeInfoDb utils stats XVector CellMapper: S4Vectors methods stats utils JunctionSeq: methods SummarizedExperiment Rcpp RcppArmadillo DESeq2 statmod Hmisc plotrix stringr Biobase locfit BiocGenerics BiocParallel genefilter geneplotter S4Vectors IRanges GenomicRanges tilingArray: Biobase methods pixmap strucchange affy vsn genefilter RColorBrewer grid stats4 vipor: stats graphics lumiHumanIDMapping: lumi methods AnnotationDbi DBI RnBeads.hg19: GenomicRanges tweeDEseqCountData: Biobase rCGH: methods stats utils graphics plyr DNAcopy lattice ggplot2 grid shiny limma affy mclust TxDb.Hsapiens.UCSC.hg18.knownGene TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene org.Hs.eg.db GenomicFeatures GenomeInfoDb GenomicRanges AnnotationDbi parallel IRanges grDevices aCGH TCC: methods DESeq2 edgeR baySeq ROC miRNAtap.db: miRNAtap AnnotationDbi DBI RSQLite softImpute: Matrix methods gptk: Matrix fields mzR: Rcpp methods utils Biobase BiocGenerics ProtGenerics ncdf4 zlibbioc Rhdf5lib NormalyzerDE: vsn preprocessCore limma MASS ape car ggplot2 methods Biobase RcmdrMisc raster utils stats SummarizedExperiment matrixStats ggforce piano: BiocGenerics Biobase gplots igraph relations marray fgsea shiny DT htmlwidgets shinyjs shinydashboard visNetwork scales grDevices graphics stats utils methods org.EcSakai.eg.db: methods AnnotationDbi dorothea: dplyr magrittr bcellViper viper affyQCReport: Biobase affy lattice affyPLM genefilter graphics grDevices RColorBrewer simpleaffy stats utils xtable mcaGUI: lattice MASS proto foreign gWidgets gWidgetsRGtk2 OTUbase vegan bpca sojourner: ggplot2 dplyr reshape2 gridExtra EBImage MASS R.matlab Rcpp fitdistrplus mclust minpack.lm mixtools mltools nls2 plyr sampSurf scales shiny shinyjs sp truncnorm utils stats pixmap rlang graphics grDevices grid compiler lattice tfprobability: tensorflow reticulate keras magrittr CNTools: methods tools stats genefilter functional: misc3d: grDevices graphics stats tcltk BrowserViz: jsonlite httpuv methods BiocGenerics BSgenome.Dmelanogaster.UCSC.dm3: BSgenome enviPat: IWTomics: GenomicRanges parallel gtable grid graphics methods IRanges KernSmooth fda S4Vectors grDevices stats utils tools BSgenome.Dmelanogaster.UCSC.dm6: BSgenome MVCClass: methods fingerprint: methods BEARscc: ggplot2 SingleCellExperiment data.table stats utils graphics compiler flowMatch: Rcpp methods flowCore Biobase prettyGraphs: sybil: Matrix lattice methods progeny: Biobase stats dplyr tidyr ggplot2 ggrepel gridExtra batchelor: SingleCellExperiment SummarizedExperiment S4Vectors BiocGenerics Rcpp stats methods utils igraph BiocNeighbors BiocSingular Matrix DelayedArray DelayedMatrixStats BiocParallel scuttle ResidualMatrix LedPred: e1071 akima ggplot2 irr jsonlite parallel plot3D plyr RCurl ROCR testthat CAFE: biovizBase GenomicRanges IRanges ggbio affy ggplot2 annotate grid gridExtra tcltk Biobase SMITE: GenomicRanges scales plyr Hmisc AnnotationDbi org.Hs.eg.db ggplot2 reactome.db KEGGREST BioNet goseq methods IRanges igraph Biobase tools S4Vectors geneLenDataBase grDevices graphics stats utils org.Bt.eg.db: methods AnnotationDbi attract: AnnotationDbi Biobase limma cluster GOstats graphics stats reactome.db KEGGREST org.Hs.eg.db utils methods scmap: Biobase SingleCellExperiment SummarizedExperiment BiocGenerics S4Vectors dplyr reshape2 matrixStats proxy utils googleVis ggplot2 methods stats e1071 randomForest Rcpp RcppArmadillo goric: nlme quadprog mvtnorm MASS Matrix parallel RCurl: methods bitops RBioinf: graph methods vtpnet: graph GenomicRanges gwascat doParallel foreach tcltk: utils gamlss.dist: MASS graphics stats methods grDevices CODEX: Rsamtools GenomeInfoDb BSgenome.Hsapiens.UCSC.hg19 IRanges Biostrings S4Vectors iBBiG: biclust stats4 xtable ade4 wordcloud: methods RColorBrewer Rcpp pathRender: graph Rgraphviz RColorBrewer cMAP AnnotationDbi methods stats4 Rserve: cowplot: ggplot2 grid gtable grDevices methods rlang scales RUVcorr: corrplot MASS stats lattice grDevices gridExtra snowfall psych BiocParallel grid bladderbatch reshape2 graphics ccdata: genomes: readr curl admisc: methods ChemmineDrugs: ChemmineR BiocGenerics RSQLite rhdf5: methods Rhdf5lib rhdf5filters ParamHelpers: backports BBmisc checkmate fastmatch methods SAGx: stats multtest methods Biobase stats4 esATAC: Rsamtools GenomicRanges ShortRead pipeFrame Rcpp methods knitr Rbowtie2 rtracklayer ggplot2 Biostrings ChIPseeker clusterProfiler igraph rJava magrittr digest BSgenome AnnotationDbi GenomicFeatures R.utils GenomeInfoDb BiocGenerics S4Vectors IRanges rmarkdown tools VennDiagram grid JASPAR2018 TFBSTools grDevices graphics stats utils parallel corrplot BiocManager motifmatchr ppcor: MASS splitstackshape: data.table wiggleplotr: dplyr ggplot2 GenomicRanges rtracklayer cowplot assertthat purrr S4Vectors IRanges GenomeInfoDb rgeos: methods sp utils stats graphics glmGamPoi: Rcpp DelayedMatrixStats matrixStats DelayedArray HDF5Array SummarizedExperiment methods stats utils splines RcppArmadillo beachmat arules: Matrix stats methods graphics utils BatchQC: utils rmarkdown knitr pander gplots MCMCpack shiny sva corpcor moments matrixStats ggvis heatmaply reshape2 limma grDevices graphics stats methods Matrix MethTargetedNGS: stringr seqinr gplots Biostrings DiffCorr: pcaMethods igraph fdrtool multtest msmsTests: MSnbase msmsEDA edgeR qvalue swfdr: methods splines stats4 stats ASEB: methods graphics utils RNAmodR.AlkAnilineSeq: RNAmodR methods S4Vectors IRanges BiocGenerics GenomicRanges Gviz org.Pf.plasmo.db: methods AnnotationDbi shinyjs: digest htmltools jsonlite shiny ExPosition: prettyGraphs ggtreeExtra: ggplot2 utils rlang ggnewscale stats ccrepe: infotheo rcompanion: stats graphics boot DescTools multcompView plyr EMT coin lmtest nortest relimp: stats utils omicade4: ade4 made4 Biobase MOFA2: rhdf5 dplyr tidyr reshape2 pheatmap ggplot2 methods GGally RColorBrewer cowplot ggrepel reticulate HDF5Array grDevices stats magrittr forcats utils corrplot DelayedArray Rtsne uwot basilisk rnaEditr: GenomicRanges IRanges BiocGenerics GenomeInfoDb bumphunter S4Vectors stats survival logistf plyr corrplot MALDIquant: methods parallel Rlab: utils SNPlocs.Hsapiens.dbSNP150.GRCh38: BSgenome methods utils BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges VplotR: GenomicRanges IRanges ggplot2 cowplot magrittr GenomeInfoDb GenomicAlignments RColorBrewer zoo Rsamtools S4Vectors parallel reshape2 methods graphics stats openssl: askpass RUVnormalize: RUVnormalizeData Biobase DNAcopy: crlmm: oligoClasses preprocessCore methods Biobase BiocGenerics affyio illuminaio ellipse mvtnorm splines stats utils lattice ff foreach RcppEigen matrixStats VGAM parallel graphics limma beanplot rPref: Rcpp RcppParallel dplyr igraph lazyeval methods utils CellMixS: kSamples BiocNeighbors ggplot2 scater viridis cowplot SummarizedExperiment SingleCellExperiment tidyr magrittr dplyr ggridges stats purrr methods BiocParallel BiocGenerics OrderedList: Biobase twilight methods poweRlaw: methods parallel pracma stats utils CHARGE: GenomicRanges methods SummarizedExperiment FactoMineR factoextra IRanges graphics modes parallel plyr cluster diptest stats matrixStats ncdfFlow: flowCore RcppArmadillo methods BH Biobase BiocGenerics zlibbioc Rcpp Rhdf5lib sincell: igraph Rcpp entropy scatterplot3d MASS TSP ggplot2 reshape2 fields proxy parallel Rtsne fastICA cluster statmod anota2seq: methods multtest qvalue limma DESeq2 edgeR RColorBrewer grDevices graphics stats utils SummarizedExperiment FField: writexl: mixsqp: utils stats irlba Rcpp RcppArmadillo MIGSAdata: 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 flexclust: graphics grid lattice modeltools methods parallel stats stats4 class knitcitations: RefManageR digest httr methods 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 TIN: data.table impute aroma.affymetrix WGCNA squash stringr xlsxjars: rJava Glimma: htmlwidgets edgeR DESeq2 limma SummarizedExperiment stats jsonlite methods S4Vectors systemPipeRdata: methods BiocGenerics jsonlite remotes RTCGA.rnaseq: RTCGA Oscope: EBSeq cluster testthat BiocParallel sscore: affy affyio netReg: tensorflow tfprobability Rcpp stats reticulate nloptr methods RcppArmadillo MetID: utils stats devtools stringr Matrix igraph ChemmineR miRcomp: Biobase miRcompData utils methods graphics KernSmooth stats rTRMui: shiny rTRM MotifDb org.Hs.eg.db org.Mm.eg.db ggraph: ggplot2 Rcpp dplyr ggforce grid igraph scales MASS digest gtable ggrepel utils stats viridis rlang tidygraph graphlayouts withr settings: grDevices graphics RcppGSL: Rcpp stats frmaExampleData: chimeraviz: Biostrings GenomicRanges IRanges Gviz S4Vectors ensembldb AnnotationFilter data.table methods grid Rsamtools GenomeInfoDb GenomicAlignments RColorBrewer graphics AnnotationDbi RCircos org.Hs.eg.db org.Mm.eg.db rmarkdown graph Rgraphviz DT plyr dplyr BiocStyle ArgumentCheck gtools magick etec16s: Biobase metagenomeSeq PoTRA: stats BiocGenerics org.Hs.eg.db igraph graph graphite pals: dichromat colorspace graphics grDevices mapproj maps methods stats spqnData: SummarizedExperiment Sushi: zoo biomaRt graphics grDevices sysfonts: clstutils: clst rjson ape lattice RSQLite Scale4C: smoothie GenomicRanges IRanges SummarizedExperiment methods grDevices graphics utils pixmap: methods graphics grDevices MWASTools: glm2 ppcor qvalue car boot grid ggplot2 gridExtra igraph SummarizedExperiment KEGGgraph RCurl KEGGREST ComplexHeatmap stats utils GladiaTOX: data.table DBI RMySQL RSQLite numDeriv RColorBrewer parallel stats methods graphics grDevices xtable tools brew stringr RJSONIO ggplot2 ggrepel tidyr utils RCurl XML munsell: colorspace methods LymphoSeq: LymphoSeqDB data.table plyr dplyr reshape VennDiagram ggplot2 ineq RColorBrewer circlize grid utils stats ggtree msa Biostrings phangorn stringdist UpSetR affylmGUI: grDevices graphics stats utils tcltk tkrplot limma affy affyio affyPLM gcrma BiocGenerics AnnotationDbi BiocManager R2HTML xtable recountmethylation: minfi HDF5Array rhdf5 S4Vectors utils methods RCurl R.utils BiocFileCache Cardinal: BiocGenerics BiocParallel EBImage graphics methods S4Vectors stats ProtGenerics Biobase dplyr irlba lattice Matrix matter magrittr mclust nlme parallel signal sp stats4 utils viridisLite microbiomeDASim: graphics ggplot2 MASS tmvtnorm Matrix mvtnorm pbapply stats phyloseq metagenomeSeq Biobase customCMPdb: AnnotationHub RSQLite XML utils ChemmineR methods stats rappdirs BiocFileCache sfsmisc: grDevices methods utils stats tools cancerdata: Biobase pamr: cluster survival RcppDate: minionSummaryData: Spectra: S4Vectors BiocParallel ProtGenerics methods IRanges MsCoreUtils graphics grDevices stats tools utils fs RNAmodR.RiboMethSeq: RNAmodR methods S4Vectors BiocGenerics IRanges GenomicRanges Gviz pairsD3: htmlwidgets shiny AssessORF: DECIPHER Biostrings GenomicRanges IRanges graphics grDevices methods stats utils alpineData: ExperimentHub GenomicAlignments utils AnnotationHub iC10TrainingData: regioneR: GenomicRanges memoise IRanges BSgenome Biostrings rtracklayer parallel graphics stats utils methods GenomeInfoDb S4Vectors tools gpuMagic: methods utils Deriv DescTools digest pryr stringr BiocGenerics Rcpp ChIPXpress: ChIPXpressData Biobase GEOquery frma affy bigmemory biganalytics AGDEX: Biobase GSEABase stats HelloRanges: methods BiocGenerics S4Vectors IRanges GenomicRanges Biostrings BSgenome GenomicFeatures VariantAnnotation Rsamtools GenomicAlignments rtracklayer GenomeInfoDb SummarizedExperiment docopt stats tools utils AnnotationHubData: methods utils S4Vectors IRanges GenomicRanges AnnotationHub GenomicFeatures Rsamtools rtracklayer BiocGenerics jsonlite BiocManager biocViews AnnotationDbi Biobase Biostrings DBI GenomeInfoDb OrganismDbi RSQLite AnnotationForge futile.logger XML RCurl fracdiff: stats panp: affy Biobase methods stats utils MEEBOdata: OpenStats: nlme MASS jsonlite Hmisc methods knitr AICcmodavg car rlist summarytools graphics stats utils rRDP: Biostrings TMB: graphics methods stats utils Matrix RcppEigen RDRToolbox: graphics grDevices methods stats MASS rgl mgcv: nlme methods stats graphics Matrix splines utils uuid: ASGSCA: Matrix MASS CINdex: GenomicRanges bitops gplots grDevices som dplyr gridExtra png stringr S4Vectors IRanges GenomeInfoDb graphics stats utils flowcatchR: methods EBImage colorRamps abind BiocParallel graphics stats utils plotly shiny GenomicFeatures: BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges AnnotationDbi methods utils stats tools DBI RSQLite RCurl XVector Biostrings rtracklayer biomaRt Biobase hpar: utils mvoutlier: sgeostat robCompositions robustbase OrganismDbi: methods BiocGenerics AnnotationDbi GenomicFeatures Biobase BiocManager GenomicRanges graph IRanges RBGL DBI S4Vectors stats aws.signature: digest base64enc ineq: stats graphics grDevices fansi: crossmeta: affy affxparser AnnotationDbi Biobase BiocGenerics BiocManager DT DBI data.table fdrtool GEOquery limma matrixStats metaMA miniUI oligo reader RColorBrewer RCurl RSQLite randomcoloR stringr sva shiny shinyjs shinyBS shinyWidgets shinypanel statmod XML readxl hwriter: gmoviz: circlize GenomicRanges graphics grid gridBase Rsamtools ComplexHeatmap BiocGenerics Biostrings GenomeInfoDb methods GenomicAlignments GenomicFeatures IRanges rtracklayer pracma colorspace S4Vectors BRGenomics: rtracklayer GenomeInfoDb S4Vectors GenomicRanges parallel IRanges stats Rsamtools GenomicAlignments DESeq2 SummarizedExperiment utils methods vroom: bit64 crayon glue hms lifecycle rlang stats tibble vctrs tidyselect withr progress cpp11 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 Glimma htmlwidgets plotly DT RTCGAToolbox: BiocGenerics data.table DelayedArray GenomicRanges GenomeInfoDb httr limma methods RaggedExperiment RCircos RCurl RJSONIO S4Vectors stats stringr SummarizedExperiment survival TCGAutils XML Harman: Rcpp graphics stats methods matlab: methods LiblineaR: methods infercnv: graphics grDevices RColorBrewer gplots futile.logger stats utils methods ape Matrix fastcluster dplyr HiddenMarkov ggplot2 edgeR coin caTools digest reshape rjags fitdistrplus future foreach doParallel BiocGenerics SummarizedExperiment SingleCellExperiment tidyr parallel coda gridExtra argparse RNifti: Rcpp alsace: ALS ptw biomvRCNS: IRanges GenomicRanges Gviz methods mvtnorm switchde: SingleCellExperiment SummarizedExperiment dplyr ggplot2 methods stats arrayQualityMetrics: affy affyPLM beadarray Biobase genefilter graphics grDevices grid gridSVG Hmisc hwriter lattice latticeExtra limma methods RColorBrewer setRNG stats utils vsn XML svglite RSeqAn: Rcpp bayNorm: Rcpp BB foreach iterators doSNOW Matrix parallel MASS locfit fitdistrplus stats methods graphics grDevices SingleCellExperiment SummarizedExperiment BiocParallel utils RcppArmadillo RcppProgress IDPmisc: methods grid lattice PerformanceAnalytics: xts methods quadprog zoo oncomix: ggplot2 ggrepel RColorBrewer mclust stats SummarizedExperiment epivizrData: methods epivizrServer Biobase S4Vectors GenomicRanges SummarizedExperiment OrganismDbi GenomicFeatures GenomeInfoDb IRanges ensembldb TxDb.Hsapiens.UCSC.hg38.knownGene: GenomicFeatures AnnotationDbi SPEM: Rsolnp Biobase methods LymphoSeqDB: LogicReg: survival stats graphics utils grDevices densityClust: Rcpp FNN Rtsne ggplot2 ggrepel grDevices gridExtra RColorBrewer clinfun: graphics stats mvtnorm adductomicsR: adductData ExperimentHub AnnotationHub parallel data.table OrgMassSpecR foreach mzR ade4 rvest pastecs reshape2 pracma DT fpc doSNOW fastcluster RcppEigen bootstrap smoother dplyr zoo stats utils graphics grDevices methods datasets iterativeBMA: BMA leaps Biobase FunChIP: GenomicRanges shiny fda doParallel GenomicAlignments Rcpp methods foreach parallel GenomeInfoDb Rsamtools grDevices graphics stats RColorBrewer CoCiteStats: org.Hs.eg.db AnnotationDbi HIBAG: methods RcppParallel sevenbridges: methods utils stats httr jsonlite yaml objectProperties stringr S4Vectors docopt curl uuid data.table Pigengene: graph bnlearn C50 MASS matrixStats partykit Rgraphviz WGCNA GO.db impute preprocessCore grDevices graphics stats utils parallel pheatmap dplyr gdata SGSeq: IRanges GenomicRanges Rsamtools SummarizedExperiment methods AnnotationDbi BiocGenerics Biostrings GenomicAlignments GenomicFeatures GenomeInfoDb RUnit S4Vectors grDevices graphics igraph parallel rtracklayer stats M3DExampleData: IsoformSwitchAnalyzeR: limma DEXSeq ggplot2 methods BSgenome plyr reshape2 gridExtra Biostrings IRanges GenomicRanges DRIMSeq RColorBrewer rtracklayer VennDiagram DBI grDevices graphics stats utils GenomeInfoDb grid tximport tximeta edgeR futile.logger stringr dplyr magrittr readr tibble XVector BiocGenerics RCurl iCheck: Biobase lumi gplots stats graphics preprocessCore grDevices randomForest affy limma parallel GeneSelectMMD rgl MASS lmtest scatterplot3d utils FIs: COSNet: rappdirs: geNetClassifier: Biobase EBarrays minet methods e1071 graphics grDevices rebus.numbers: rebus.base utils Cairo: grDevices graphics MeSH.Hsa.eg.db: MeSHDbi RcwlPipelines: Rcwl BiocFileCache rappdirs methods utils ribor: dplyr ggplot2 hash methods rhdf5 rlang stats S4Vectors tidyr tools yaml TxDb.Mmusculus.UCSC.mm10.knownGene: GenomicFeatures AnnotationDbi ssPATHS: SummarizedExperiment ROCR dml MESS GCSscore: BiocManager Biobase utils methods RSQLite devtools dplR stringr graphics stats affxparser data.table velociraptor: SummarizedExperiment methods stats Matrix BiocGenerics reticulate S4Vectors DelayedArray basilisk zellkonverter scuttle SingleCellExperiment BiocParallel BiocSingular SeuratObject: grDevices grid Matrix methods Rcpp rlang sctransform stats tools utils RcppEigen httpuv: Rcpp utils R6 promises later R2jags: rjags abind coda graphics grDevices methods R2WinBUGS parallel stats utils TreeSummarizedExperiment: SingleCellExperiment S4Vectors methods BiocGenerics utils ape rlang dplyr SummarizedExperiment COSMIC.67: GenomicRanges SummarizedExperiment VariantAnnotation Nozzle.R1: org.Rn.eg.db: methods AnnotationDbi ROSeq: pbmcapply edgeR limma BSgenome.Mmusculus.UCSC.mm8: BSgenome GenKern: KernSmooth utils BSgenome.Mmusculus.UCSC.mm9: BSgenome 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 DeconRNASeq: limSolve pcaMethods ggplot2 grid cytomapper: EBImage SingleCellExperiment methods S4Vectors RColorBrewer viridis utils SummarizedExperiment tools graphics raster grDevices stats ggplot2 ggbeeswarm svgPanZoom svglite shiny shinydashboard matrixStats TurboNorm: convert limma marray stats grDevices affy lattice babelgene: dplyr methods rlang CORREP: e1071 stats matchingR: Rcpp RcppArmadillo CoreGx: Biobase S4Vectors SummarizedExperiment piano BiocParallel BiocGenerics methods stats utils graphics grDevices lsa data.table crayon bumphunter: S4Vectors IRanges GenomeInfoDb GenomicRanges foreach iterators methods parallel locfit matrixStats limma doRNG BiocGenerics utils GenomicFeatures AnnotationDbi stats FunciSNP: ggplot2 TxDb.Hsapiens.UCSC.hg19.knownGene FunciSNP.data methods BiocGenerics Biobase S4Vectors IRanges GenomicRanges Rsamtools rtracklayer ChIPpeakAnno VariantAnnotation plyr snpStats reshape scales ggsci: grDevices scales ggplot2 spsUtil: httr assertthat stringr glue magrittr crayon utils tiff: fCCAC: S4Vectors IRanges GenomicRanges grid fda RColorBrewer genomation ggplot2 ComplexHeatmap grDevices stats utils credentials: openssl sys curl jsonlite askpass SNPlocs.Hsapiens.dbSNP141.GRCh38: S4Vectors IRanges GenomeInfoDb GenomicRanges BSgenome methods utils permute: stats specL: DBI methods protViz RSQLite seqinr hgfocusprobe: AnnotationDbi SPIA: graphics KEGGgraph matrixcalc: UMI4Cats: SummarizedExperiment magick cowplot scales GenomicRanges ShortRead zoo ggplot2 reshape2 regioneR IRanges S4Vectors magrittr dplyr BSgenome Biostrings DESeq2 R.utils Rsamtools stringr Rbowtie2 methods GenomeInfoDb GenomicAlignments RColorBrewer utils grDevices stats org.Hs.eg.db annotate TxDb.Hsapiens.UCSC.hg19.knownGene rlang GenomicFeatures BiocFileCache rappdirs fda base64: openssl HDF5Array: methods DelayedArray rhdf5 utils stats tools Matrix BiocGenerics S4Vectors IRanges Rhdf5lib binom: rnaseqcomp: RColorBrewer methods blme: lme4 methods stats utils speaq: MassSpecWavelet cluster mQTL parallel doSNOW data.table foreach stats Rfast utils graphics grDevices ggplot2 gridExtra reshape2 rvest xml2 missForest impute ada: rpart hash: methods utils FNN: human.db0: methods AnnotationDbi Prize: diagram stringr ggplot2 reshape2 grDevices matrixcalc stats gplots methods utils graphics TargetScoreData: venn: admisc goseq: BiasedUrn geneLenDataBase mgcv graphics stats utils AnnotationDbi GO.db BiocGenerics randRotation: methods graphics utils stats Rdpack tkrplot: grDevices tcltk Rqc: BiocParallel ShortRead ggplot2 BiocGenerics Biostrings IRanges methods S4Vectors knitr BiocStyle plyr markdown grid reshape2 Rcpp biovizBase shiny Rsamtools GenomicAlignments GenomicFiles openPrimeR: Biostrings XML scales reshape2 seqinr IRanges GenomicRanges ggplot2 plyr dplyr stringdist stringr RColorBrewer DECIPHER lpSolveAPI digest Hmisc ape BiocGenerics S4Vectors foreach magrittr distr distrEx fitdistrplus uniqtag openxlsx grid grDevices stats utils methods shades: erccdashboard: ggplot2 gridExtra edgeR gplots grid gtools limma locfit MASS plyr qvalue reshape2 ROCR scales stringr aroma.light: stats R.methodsS3 R.oo R.utils matrixStats blockmodeling: stats methods Matrix parallel GWENA: WGCNA dplyr dynamicTreeCut ggplot2 gprofiler2 magrittr tibble tidyr NetRep igraph RColorBrewer purrr rlist matrixStats SummarizedExperiment stringr methods graphics stats utils proj4: PROPS: bnlearn reshape2 sva stats utils Biobase microbenchmark: graphics stats BUSpaRse: AnnotationDbi AnnotationFilter biomaRt BiocGenerics Biostrings BSgenome dplyr ensembldb GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges magrittr Matrix methods plyranges Rcpp S4Vectors stats stringr tibble tidyr utils zeallot RcppArmadillo RcppProgress BH synlet: ggplot2 doBy dplyr grid magrittr RColorBrewer RankProd reshape2 cubature: Rcpp investr: base graphics nlme stats utils geneClassifiers: utils methods stats Biobase BiocGenerics Uniquorn: stringr R.utils WriteXLS stats doParallel foreach GenomicRanges IRanges VariantAnnotation TSP: graphics foreach utils stats grDevices prada: Biobase RColorBrewer grid methods rrcov BiocGenerics graphics grDevices MASS stats4 utils blob: methods rlang vctrs pipeFrame: BSgenome digest visNetwork magrittr methods Biostrings GenomeInfoDb parallel stats utils MCMCpack: coda MASS stats graphics grDevices lattice methods utils mcmc quantreg blima: beadarray Biobase Rcpp BiocGenerics grDevices stats graphics affyPLM: BiocGenerics affy Biobase gcrma stats preprocessCore zlibbioc graphics grDevices methods R.devices: grDevices R.methodsS3 R.oo R.utils base64enc rjags: coda gProfileR: RCurl plyr utils spatstat.geom: spatstat.data stats graphics grDevices utils methods spatstat.utils deldir polyclip rapidjsonr: argparse: R6 findpython jsonlite affyContam: tools methods utils Biobase affy affydata minpack.lm: geneRecommender: Biobase methods stats BGmix: KernSmooth DMRcate: minfi SummarizedExperiment ExperimentHub bsseq GenomeInfoDb limma edgeR DSS missMethyl GenomicRanges methods graphics plyr Gviz IRanges stats utils S4Vectors TTR: xts zoo curl ChIPseqR: methods BiocGenerics S4Vectors Biostrings fBasics GenomicRanges IRanges graphics grDevices HilbertVis ShortRead stats timsac utils iASeq: graphics grDevices similaRpeak: R6 stats fgsea: Rcpp data.table BiocParallel stats ggplot2 gridExtra grid fastmatch Matrix utils BH paintmap: filehash: methods AlpsNMR: dplyr future magrittr utils graphics stats grDevices signal assertthat rlang stringr tibble tidyr readxl plyr purrr glue reshape2 GGally mixOmics matrixStats writexl fs rmarkdown speaq htmltools ggrepel pcaPP furrr ggplot2 baseline zip tidyselect BiocParallel SummarizedExperiment S4Vectors recount: SummarizedExperiment BiocParallel derfinder downloader GEOquery GenomeInfoDb GenomicRanges IRanges methods RCurl rentrez rtracklayer S4Vectors stats utils RRHO: grid VennDiagram bitops: BayesSpace: SingleCellExperiment Rcpp stats purrr scater scran SummarizedExperiment coda rhdf5 S4Vectors Matrix assertthat mclust RCurl DirichletReg xgboost utils ggplot2 scales BiocFileCache RcppArmadillo RcppDist RcppProgress MeSH.Syn.eg.db: MeSHDbi hypeR: ggplot2 ggforce R6 magrittr dplyr purrr stats stringr scales rlang httr openxlsx htmltools reshape2 reactable msigdbr kableExtra rmarkdown igraph visNetwork shiny clipr: utils geneRxCluster: GenomicRanges IRanges biclust: MASS grid colorspace lattice methods flexclust additivityTests tidyr ggplot2 qcmetrics: Biobase methods knitr tools Nozzle.R1 xtable pander S4Vectors prodlim: Rcpp stats grDevices graphics survival KernSmooth lava MSstatsBioData: SNPlocs.Hsapiens.dbSNP142.GRCh37: IRanges GenomeInfoDb GenomicRanges BSgenome methods utils slingshot: princurve stats ape graphics grDevices igraph matrixStats methods SingleCellExperiment SummarizedExperiment viridisLite: msImpute: softImpute methods stats graphics pdist reticulate scran data.table FNN matrixStats rdetools limma mvtnorm setRNG: tomoda: methods stats grDevices reshape2 Rtsne umap RColorBrewer ggplot2 ggrepel SummarizedExperiment statip: clue graphics rpart stats gageData: muscat: BiocParallel blme ComplexHeatmap data.table DESeq2 dplyr edgeR ggplot2 glmmTMB grDevices grid limma lmerTest lme4 Matrix matrixStats methods progress purrr S4Vectors scales scater sctransform stats SingleCellExperiment SummarizedExperiment variancePartition viridis spatstat.utils: stats graphics grDevices utils methods DAPAR: Biobase MSnbase tibble RColorBrewer stats preprocessCore Cairo png lattice reshape2 gplots pcaMethods ggplot2 limma knitr tmvtnorm norm impute stringr grDevices graphics openxlsx utils cp4p scales Matrix vioplot imp4p forcats methods highcharter DAPARdata siggenes graph lme4 readxl clusterProfiler dplyr tidyr AnnotationDbi tidyverse vsn FactoMineR factoextra multcomp purrr visNetwork foreach parallel doParallel igraph dendextend Mfuzz apcluster diptest cluster ChIPexoQualExample: scTHI.data: focalCall: CGHcall Rwave: GraphAlignment: DiffLogo: stats cba grDevices graphics utils tools MSstatsTMT: limma lme4 lmerTest dplyr tidyr statmod methods reshape2 data.table matrixStats stats utils ggplot2 grDevices graphics MSstats doseR: edgeR methods stats graphics matrixStats mclust lme4 RUnit SummarizedExperiment digest S4Vectors zellkonverter: Matrix basilisk reticulate SingleCellExperiment SummarizedExperiment DelayedArray methods S4Vectors utils grid: grDevices utils flowPeaks: BB: stats quadprog nsga2R: mco NormqPCR: stats RColorBrewer Biobase methods ReadqPCR qpcR SimFFPE: Biostrings dplyr foreach doParallel truncnorm GenomicRanges IRanges Rsamtools parallel graphics stats utils methods feather: Rcpp tibble hms VariantAnnotation: methods BiocGenerics MatrixGenerics GenomeInfoDb GenomicRanges SummarizedExperiment Rsamtools utils DBI zlibbioc Biobase S4Vectors IRanges XVector Biostrings AnnotationDbi rtracklayer BSgenome GenomicFeatures Rhtslib metaSeq: NOISeq snow Rcpp projectR: methods cluster stats limma CoGAPS NMF ROCR ggalluvial RColorBrewer dplyr reshape2 viridis scales ggplot2 waddR: Rcpp arm BiocFileCache BiocParallel SingleCellExperiment parallel methods stats RcppArmadillo askpass: sys BH: BioNetStat: shiny igraph shinyBS pathview DT BiocParallel RJSONIO whisker yaml pheatmap ggplot2 plyr utils stats RColorBrewer Hmisc psych knitr rmarkdown markdown vioplot: sm zoo SNPlocs.Hsapiens.dbSNP144.GRCh37: BSgenome methods utils BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges SNPlocs.Hsapiens.dbSNP144.GRCh38: BSgenome methods utils BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges feature: ks plot3D tcltk GOTHiC: methods GenomicRanges Biostrings BSgenome data.table BiocGenerics S4Vectors IRanges Rsamtools ShortRead rtracklayer ggplot2 BiocManager grDevices utils stats GenomeInfoDb bayesm: Rcpp utils stats graphics grDevices RcppArmadillo poilog: maptools: sp foreign methods grid lattice stats utils grDevices RSNNS: methods Rcpp splineTimeR: Biobase igraph limma GSEABase gtools splines GeneNet longitudinal FIs MassArray: methods graphics grDevices stats utils RcppRoll: Rcpp OTUbase: methods S4Vectors IRanges ShortRead Biobase vegan Biostrings RProtoBufLib: GEM: tcltk ggplot2 methods stats grDevices graphics utils ipred: rpart MASS survival nnet class prodlim GFA: profvis: htmlwidgets stringr flowPloidyData: AneuFinder: GenomicRanges ggplot2 cowplot AneuFinderData methods utils grDevices graphics stats foreach doParallel BiocGenerics S4Vectors GenomeInfoDb IRanges Rsamtools bamsignals DNAcopy ecp Biostrings GenomicAlignments reshape2 ggdendro ggrepel ReorderCluster mclust NetPathMiner: igraph DEGseq: qvalue methods graphics grDevices stats utils weitrix: SummarizedExperiment methods utils stats grDevices assertthat S4Vectors DelayedArray DelayedMatrixStats BiocParallel BiocGenerics limma topconfects dplyr purrr ggplot2 rlang scales reshape2 splines Ckmeans.1d.dp glm2 RhpcBLASctl tinytex: xfun a4Classif: a4Core a4Preproc methods Biobase ROCR pamr glmnet varSelRF utils graphics stats 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 sparsepca: rsvd test3cdf: utils AnnotationDbi CNAnorm: methods DNAcopy nabor: Rcpp methods RcppEigen BH breastCancerMAINZ: antiProfiles: matrixStats methods locfit flowAI: ggplot2 flowCore plyr changepoint knitr reshape2 RColorBrewer scales methods graphics stats utils rmarkdown pd.mapping250k.sty: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors 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 HIPPO: ggplot2 graphics stats reshape2 gridExtra Rtsne umap dplyr rlang magrittr irlba Matrix SingleCellExperiment ggrepel hierGWAS: fastcluster glmnet fmsb primirTSS: GenomicRanges S4Vectors rtracklayer dplyr stringr tidyr Biostrings purrr BSgenome.Hsapiens.UCSC.hg38 phastCons100way.UCSC.hg38 GenomicScores shiny Gviz BiocGenerics IRanges TFBSTools JASPAR2018 tibble R.utils stats utils sampleClassifierData: SummarizedExperiment DT: htmltools htmlwidgets jsonlite magrittr crosstalk promises derfinderData: ReorderCluster: gplots graphics Rcpp DriverNet: methods praznik: RMallow: combinat GeuvadisTranscriptExpr: Affyhgu133aExpr: AWFisher: edgeR limma stats additivityTests: BASiCS: SingleCellExperiment Biobase BiocGenerics coda cowplot ggExtra ggplot2 graphics grDevices MASS methods Rcpp S4Vectors scran stats stats4 SummarizedExperiment viridis utils Matrix matrixStats assertthat reshape2 BiocParallel hexbin RcppArmadillo MAGeCKFlute: Biobase clusterProfiler enrichplot gridExtra ggplot2 ggrepel grDevices grid reshape2 stats utils breastCancerTRANSBIG: ecolitk: Biobase graphics methods mgsa: methods gplots graphics stats utils OUTRIDER: BiocParallel GenomicFeatures SummarizedExperiment data.table methods BBmisc BiocGenerics DESeq2 generics GenomicRanges ggplot2 grDevices heatmaply pheatmap graphics IRanges matrixStats plotly plyr pcaMethods PRROC RColorBrewer Rcpp reshape2 S4Vectors scales splines stats utils RcppArmadillo ontologyPlot: methods ontologyIndex paintmap Rgraphviz numDeriv: oposSOM: igraph fastICA tsne scatterplot3d pixmap fdrtool ape biomaRt Biobase RcppParallel Rcpp bbmle: stats4 stats numDeriv lattice MASS methods bdsmatrix Matrix mvtnorm doSNOW: foreach iterators snow utils coseq: SummarizedExperiment S4Vectors edgeR DESeq2 capushe Rmixmod e1071 BiocParallel ggplot2 scales HTSFilter corrplot HTSCluster grDevices graphics stats methods compositions mvtnorm human370v1cCrlmm: utils GWASExactHW: HCAExplorer: dplyr BiocFileCache HCAMatrixBrowser S4Vectors LoomExperiment vctrs curl httr jsonlite methods plyr readr rlang tibble tidygraph utils xml2 SRGnet: EBcoexpress MASS igraph pvclust gbm limma DMwR matrixStats Hmisc MiPP: Biobase e1071 MASS stats HiddenMarkov: ISAnalytics: magrittr utils reactable htmltools dplyr readr tidyr purrr rlang forcats tibble BiocParallel stringr fs zip lubridate lifecycle ggplot2 ggrepel stats upsetjs psych grDevices data.table readxl tools ore: DMRScan: Matrix MASS RcppRoll GenomicRanges IRanges GenomeInfoDb methods mvtnorm stats parallel r3Cseq: GenomicRanges Rsamtools rtracklayer VGAM qvalue methods GenomeInfoDb IRanges Biostrings data.table sqldf RColorBrewer GA: methods foreach iterators stats graphics grDevices utils cli crayon Rcpp RcppArmadillo scFeatureFilter: dplyr ggplot2 magrittr rlang tibble stats methods stats4: graphics methods stats inum: stats libcoin iheatmapr: methods utils magrittr stats ggdendro fastcluster RColorBrewer htmlwidgets jsonlite scales knitr tools flowCL: Rgraphviz SPARQL methods grDevices utils graph AnnotationDbi: methods utils stats4 BiocGenerics Biobase IRanges DBI RSQLite S4Vectors propr: methods fastcluster ggplot2 grDevices igraph Rcpp stats utils aod: methods stats LACE: graphics grDevices igraph parallel RColorBrewer Rfast stats SummarizedExperiment utils pcaPP: mvtnorm bluster: stats methods utils Matrix Rcpp igraph S4Vectors BiocParallel BiocNeighbors protolite: Rcpp jsonlite flowPlots: methods flowSpecs: ggplot2 BiocGenerics BiocParallel Biobase reshape2 flowCore zoo stats methods assertive.models: assertive.base stats extrafont: extrafontdb grDevices utils Rttf2pt1 BasicSTARRseq: GenomicRanges GenomicAlignments S4Vectors methods IRanges GenomeInfoDb stats varSelRF: randomForest parallel reprex: callr cli clipr fs glue knitr rlang rmarkdown rstudioapi utils withr CytoTree: igraph FlowSOM Rtsne ggplot2 destiny gmodels flowUtils Biobase Matrix flowCore sva matrixStats methods mclust prettydoc RANN Rcpp BiocNeighbors cluster pheatmap scatterpie umap scatterplot3d limma stringr grDevices grid stats mosaicsExample: ToPASeq: graphite Rcpp graph methods Biobase RBGL SummarizedExperiment gRbase limma corpcor ramwas: methods filematrix graphics stats utils digest glmnet KernSmooth grDevices GenomicAlignments Rsamtools parallel biomaRt Biostrings BiocGenerics ape: nlme lattice graphics methods stats tools utils parallel Rcpp HH: lattice stats grid latticeExtra multcomp gridExtra graphics reshape2 leaps vcd colorspace RColorBrewer shiny Hmisc abind Rmpfr grDevices methods immunoClust: flowCore methods stats graphics grid lattice grDevices GenomeInfoDb: methods BiocGenerics S4Vectors IRanges stats stats4 utils RCurl GenomeInfoDbData latticeExtra: lattice grid stats utils grDevices png jpeg RColorBrewer netbiov: igraph SICtools: methods Rsamtools doParallel Biostrings stringr matrixStats plyr GenomicRanges IRanges scuttle: SingleCellExperiment methods utils stats Matrix Rcpp BiocGenerics S4Vectors BiocParallel GenomicRanges SummarizedExperiment DelayedArray DelayedMatrixStats beachmat TxDb.Scerevisiae.UCSC.sacCer3.sgdGene: GenomicFeatures AnnotationDbi rhdf5client: methods DelayedArray S4Vectors httr R6 rjson utils kknn: igraph Matrix stats graphics lpsymphony: idiogram: methods Biobase annotate plotrix logger: utils pcaExplorer: DESeq2 SummarizedExperiment GenomicRanges IRanges S4Vectors genefilter ggplot2 heatmaply plotly scales NMF plyr topGO limma GOstats GO.db AnnotationDbi shiny shinydashboard shinyBS ggrepel DT shinyAce threejs biomaRt pheatmap knitr rmarkdown base64enc tidyr grDevices methods cgdsr: R.oo R.methodsS3 httr ENCODExplorer: methods tools jsonlite RCurl tidyr data.table dplyr stringr stringi utils AnnotationHub GenomicRanges rtracklayer S4Vectors GenomeInfoDb ENCODExplorerData downlit: brio digest evaluate fansi rlang vctrs yaml macat: Biobase annotate cellbaseR: methods jsonlite httr data.table pbapply tidyr R.utils Rsamtools BiocParallel foreach utils parallel doParallel RmiR: RmiR.Hs.miRNA RSVGTipsDevice DBI methods stats rfPred: Rsamtools GenomicRanges IRanges data.table methods parallel ismev: mgcv SCBN: stats org.Pt.eg.db: methods AnnotationDbi IsoCorrectoRGUI: IsoCorrectoR readxl tcltk2 tcltk utils biomformat: methods plyr jsonlite Matrix rhdf5 enrichplot: cowplot DOSE ggplot2 ggraph graphics grid igraph methods plyr purrr RColorBrewer reshape2 stats utils scatterpie shadowtext GOSemSim magrittr GWAS.BAYES: Rcpp RcppEigen GA caret ggplot2 doParallel memoise reshape2 Matrix survMisc: survival graphics grDevices stats utils knitr KMsurv ggplot2 data.table zoo grid gridExtra km.ci xtable microbiomeExplorer: shiny magrittr metagenomeSeq Biobase shinyjs shinydashboard shinycssloaders shinyWidgets rmarkdown DESeq2 RColorBrewer dplyr tidyr rlang knitr readr DT biomformat tools stringr vegan matrixStats heatmaply car broom limma reshape2 tibble forcats lubridate methods plotly circular: stats boot mvtnorm klaR: MASS combinat questionr grDevices stats utils graphics hicrep: stats rhdf5 Rcpp rmarkdown testthat strawr DelayedMatrixStats: MatrixGenerics DelayedArray methods matrixStats sparseMatrixStats Matrix S4Vectors IRanges HDF5Array BiocParallel MatrixModels: stats methods Matrix Autotuner: methods Biobase MSnbase RColorBrewer mzR assertthat scales entropy cluster grDevices graphics stats utils MOSim: HiddenMarkov zoo methods matrixStats dplyr stringi lazyeval rlang stats utils purrr scales stringr tibble tidyr ggplot2 Biobase IRanges S4Vectors flowFP: flowCore flowViz Biobase BiocGenerics graphics grDevices methods stats stats4 SLqPCR: stats BoolNet: igraph XML slam: stats missMDA: FactoMineR ggplot2 graphics grDevices mice mvtnorm stats utils doParallel parallel foreach listviewer: htmltools htmlwidgets shiny gaggle: rJava graph RUnit ggpubr: ggplot2 ggrepel grid ggsci stats utils tidyr purrr dplyr cowplot ggsignif scales gridExtra glue polynom rlang rstatix tibble magrittr LPEadj: LPE stats pathprint: stats utils arm: MASS Matrix stats lme4 abind coda graphics grDevices Hmisc methods nlme utils muscle: Biostrings LowMACA: cgdsr parallel stringr reshape2 data.table RColorBrewer methods LowMACAAnnotation BiocParallel motifStack Biostrings httr grid gridBase proto: SAIGEgds: gdsfmt SeqArray Rcpp methods stats utils RcppParallel SPAtest RcppArmadillo mCSEA: mCSEAdata Homo.sapiens biomaRt fgsea GenomicFeatures GenomicRanges ggplot2 graphics grDevices Gviz IRanges limma methods parallel S4Vectors stats SummarizedExperiment utils questionr: shiny miniUI rstudioapi highr styler classInt htmltools graphics stats utils labelled TissueEnrich: ensurer ggplot2 SummarizedExperiment GSEABase dplyr tidyr stats apcluster: Rcpp methods Matrix stats graphics grDevices clustComp: sm stats graphics grDevices 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 MPINet: BiasedUrn mgcv multipanelfigure: assertive.base assertive.files assertive.numbers assertive.properties assertive.types ggplot2 grid gridGraphics gtable magick magrittr stats stringi utils data.tree: R6 stringi methods rae230a.db: methods AnnotationDbi org.Rn.eg.db mutoss: mvtnorm plotrix multtest multcomp methods geometry: magic Rcpp lpSolve linprog RcppProgress trackViewer: grDevices methods GenomicRanges grid GenomeInfoDb GenomicAlignments GenomicFeatures Gviz Rsamtools S4Vectors rtracklayer BiocGenerics scales tools IRanges AnnotationDbi grImport htmlwidgets plotrix Rgraphviz InteractionSet graph utils ClusterJudge: stats utils graphics infotheo lattice latticeExtra httr jsonlite ash: scTHI: BiocParallel Rtsne grDevices graphics stats glpkAPI: methods RSQLite: bit64 blob DBI memoise methods pkgconfig Rcpp plogr simpleaffy: methods utils grDevices graphics stats BiocGenerics Biobase affy genefilter gcrma breakpointR: GenomicRanges cowplot breakpointRdata methods utils grDevices stats S4Vectors GenomeInfoDb IRanges Rsamtools GenomicAlignments ggplot2 BiocGenerics gtools doParallel foreach hgu133atagcdf: utils AnnotationDbi metaMA: limma SMVar SeqSQC: ExperimentHub SNPRelate e1071 GenomicRanges gdsfmt ggplot2 GGally IRanges methods rbokeh RColorBrewer reshape2 rmarkdown S4Vectors stats utils ranger: Rcpp Matrix RcppEigen LOLA: BiocGenerics S4Vectors IRanges GenomicRanges data.table reshape2 utils stats methods oligoClasses: BiocGenerics Biobase methods graphics IRanges GenomicRanges SummarizedExperiment Biostrings affyio foreach BiocManager utils S4Vectors RSQLite DBI ff Deriv: methods SCFA: matrixStats keras tensorflow BiocParallel igraph Matrix cluster clusterCrit psych glmnet RhpcBLASctl stats utils methods survival proBatch: Biobase corrplot dplyr data.table ggfortify ggplot2 grDevices lazyeval lubridate magrittr pheatmap preprocessCore purrr pvca RColorBrewer reshape2 rlang scales stats sva tidyr tibble tools utils viridis wesanderson WGCNA bslib: grDevices htmltools jsonlite sass digest jquerylib rlang magrittr rcellminer: Biobase rcellminerData stringr gplots ggplot2 methods stats utils shiny QDNAseq.hg19: QDNAseq INSPEcT: methods Biobase BiocParallel pROC deSolve rootSolve KernSmooth gdata GenomicFeatures GenomicRanges IRanges BiocGenerics GenomicAlignments Rsamtools S4Vectors GenomeInfoDb DESeq2 plgem rtracklayer SummarizedExperiment TxDb.Mmusculus.UCSC.mm9.knownGene shiny SOMbrero: igraph markdown scatterplot3d shiny grDevices graphics stats ggplot2 ggwordcloud metR interp riboSeqR: methods GenomicRanges abind Rsamtools IRanges baySeq GenomeInfoDb seqLogo bookdown: htmltools knitr rmarkdown xfun tinytex yaml ggforce: ggplot2 Rcpp grid scales MASS tweenr gtable rlang polyclip stats grDevices tidyselect withr utils RcppEigen metaMS: methods CAMERA xcms Matrix tools robustbase BiocGenerics graphics stats utils survtype: SummarizedExperiment pheatmap survival survminer clustvarsel stats utils emdist: ic.infer: quadprog mvtnorm boot kappalab bioDist: methods Biobase KernSmooth distrEx: methods distr startupmsg utils stats r2glmm: mgcv lmerTest Matrix pbkrtest ggplot2 afex stats MASS gridExtra grid data.table dplyr GPA: methods graphics Rcpp parallel ggplot2 ggrepel plyr vegan DT shiny shinyBS stats utils grDevices vidger: Biobase DESeq2 edgeR GGally ggplot2 ggrepel knitr RColorBrewer rmarkdown scales stats SummarizedExperiment tidyr utils BayesKnockdown: stats Biobase ImpulseDE2: Biobase BiocParallel ComplexHeatmap circlize compiler cowplot DESeq2 ggplot2 grDevices knitr Matrix methods S4Vectors stats SummarizedExperiment utils 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 diffloopdata: CpGassoc: nlme methods Metab: xcms svDialogs pander DynDoc: methods utils BiocFileCache: dbplyr methods stats utils dplyr RSQLite DBI rappdirs curl httr flowMeans: Biobase graphics grDevices methods rrcov stats feature flowCore keggorthology: stats graph hgu95av2.db AnnotationDbi DBI grDevices methods tools utils NanoStringQCPro: methods AnnotationDbi org.Hs.eg.db Biobase knitr NMF RColorBrewer png panelcn.mops: cn.mops methods utils stats graphics GenomicRanges Rsamtools IRanges S4Vectors GenomeInfoDb grDevices glasso: JctSeqData: pwrEWAS.data: ExperimentHub SNPhood: GenomicRanges Rsamtools data.table checkmate DESeq2 cluster ggplot2 lattice GenomeInfoDb BiocParallel VariantAnnotation BiocGenerics IRanges methods SummarizedExperiment RColorBrewer Biostrings grDevices gridExtra stats grid utils reshape2 scales S4Vectors distinct: Rcpp stats SummarizedExperiment SingleCellExperiment methods Matrix foreach parallel doParallel doRNG ggplot2 limma scater RcppArmadillo stageR: SummarizedExperiment methods stats KEGGgraph: methods XML graph utils RCurl relations: cluster stats slam sets graphics grDevices osfr: crul jsonlite stringi purrr tibble rlang fs memoise httr HTMLUtils: R2HTML iSeq: rsnps: plyr stringr crul data.table jsonlite RJSONIO httr BEAT: GenomicRanges ShortRead Biostrings BSgenome rematch: SRAdb: RSQLite graph RCurl GEOquery base64enc: WebGestaltR: methods dplyr doRNG readr parallel doParallel foreach jsonlite httr rlang svglite igraph whisker apcluster Rcpp siggenes: Biobase multtest splines methods stats4 grDevices graphics stats scrime shinyhelper: shiny markdown cellity: AnnotationDbi e1071 ggplot2 graphics grDevices grid mvoutlier org.Hs.eg.db org.Mm.eg.db robustbase stats topGO utils MAQCsubsetAFX: affy Biobase wheatmap: grid stats colorspace RColorBrewer dbplyr: assertthat blob DBI dplyr ellipsis glue lifecycle magrittr methods purrr R6 rlang tibble tidyselect utils vctrs withr phemd: monocle SingleCellExperiment RColorBrewer igraph transport pracma cluster Rtsne destiny Seurat RANN ggplot2 maptree pheatmap scatterplot3d VGAM methods grDevices graphics stats utils cowplot S4Vectors BiocGenerics SummarizedExperiment Biobase phateR reticulate Repitools: methods BiocGenerics parallel S4Vectors IRanges GenomeInfoDb GenomicRanges Biostrings Rsamtools GenomicAlignments rtracklayer BSgenome gplots grid MASS gsmoothr edgeR DNAcopy Ringo Rsolnp cluster proxy: stats utils affycoretools: Biobase methods affy limma GOstats gcrma splines xtable AnnotationDbi ggplot2 gplots oligoClasses ReportingTools hwriter lattice S4Vectors edgeR RSQLite BiocGenerics DBI Glimma GCSFilesystem: stats ngsReports: BiocGenerics ggplot2 tibble Biostrings checkmate dplyr DT FactoMineR forcats ggdendro grDevices grid lifecycle lubridate methods pander parallel plotly readr reshape2 rmarkdown Rsamtools scales ShortRead stats stringr tidyr tidyselect utils viridisLite zoo Affyhgu133Plus2Expr: sights: MASS qvalue ggplot2 reshape2 lattice stats rncl: Rcpp progress stats sourcetools: tidytree: ape dplyr lazyeval magrittr methods rlang tibble utils geeM: Matrix stats methods peakPantheR: foreach doParallel ggplot2 gridExtra MSnbase mzR stringr methods XML minpack.lm scales shiny shinythemes shinycssloaders DT utils mixtools: kernlab MASS segmented stats survival PhyloProfile: ape bioDist BiocStyle Biostrings colourpicker data.table DT energy ExperimentHub ggplot2 gridExtra pbapply RColorBrewer shiny shinyBS shinyjs OmaDB plyr xml2 zoo GEOmap: RPMG splancs fields MBA aws: awsMethods methods gsl crayon: grDevices methods utils gclus: cluster ffpe: TTR methods Biobase BiocGenerics affy lumi methylumi sfsmisc RNAprobR: GenomicFeatures plyr BiocGenerics Biostrings GenomicRanges IRanges Rsamtools rtracklayer GenomicAlignments S4Vectors graphics stats utils yaml: UNDO: methods BiocGenerics Biobase MASS boot nnls stats utils GIGSEA: Matrix MASS locfdr stats utils GSA: bgx: Biobase affy gcrma Rcpp ggupset: ggplot2 gtable grid tibble rlang scales fabia: Biobase methods graphics grDevices stats utils pipeComp: BiocParallel S4Vectors ComplexHeatmap SingleCellExperiment SummarizedExperiment Seurat matrixStats Matrix cluster aricode methods utils dplyr grid scales scran viridisLite clue randomcoloR ggplot2 cowplot intrinsicDimension scater knitr reshape2 stats Rtsne uwot circlize RColorBrewer RNAinteract: abind locfit Biobase RColorBrewer ICS ICSNP cellHTS2 geneplotter gplots grid hwriter lattice latticeExtra limma methods splots ChIPsim: Biostrings IRanges XVector ShortRead graphics methods stats utils reshape2: plyr Rcpp stringr bnbc: methods BiocGenerics SummarizedExperiment GenomicRanges Rcpp IRanges rhdf5 data.table GenomeInfoDb S4Vectors matrixStats preprocessCore sva parallel EBImage utils rJava: methods plotROC: ggplot2 methods grid gridSVG shiny plyr rlang psichomics: shiny shinyBS AnnotationDbi AnnotationHub BiocFileCache cluster colourpicker data.table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel graphics grDevices highcharter htmltools httr jsonlite limma pairsD3 plyr Rcpp recount Rfast R.utils reshape2 shinyjs stringr stats SummarizedExperiment survival tools utils XML xtable methods org.Hs.eg.db GGtools: GGBase data.table parallel Homo.sapiens methods utils stats BiocGenerics snpStats ff Rsamtools AnnotationDbi Biobase bit VariantAnnotation hexbin rtracklayer Gviz stats4 S4Vectors IRanges GenomeInfoDb GenomicRanges iterators Biostrings ROCR biglm ggplot2 reshape2 cnvGSA: brglm doParallel foreach GenomicRanges methods splitstackshape sarks: rJava Biostrings IRanges utils stats cluster binom R6: CRImage: EBImage DNAcopy aCGH MASS e1071 foreach sgeostat urltools: Rcpp methods triebeard cellscape: htmlwidgets jsonlite reshape2 stringr plyr dplyr gtools sesame: sesameData methods BiocParallel grDevices utils stringr tibble illuminaio MASS GenomicRanges IRanges grid preprocessCore S4Vectors randomForest wheatmap ggplot2 parallel matrixStats DNAcopy stats SummarizedExperiment pls: grDevices graphics methods stats Rmpi: parallel PharmacoGx: CoreGx Biobase S4Vectors SummarizedExperiment BiocParallel ggplot2 magicaxis RColorBrewer parallel caTools methods downloader stats utils graphics grDevices reshape2 jsonlite data.table units: Rcpp plot3D: misc3d stats graphics grDevices methods RcisTarget: AUCell BiocGenerics data.table feather graphics GSEABase methods R.utils stats SummarizedExperiment utils qpcR: MASS minpack.lm rgl robustbase Matrix methods pmm: lme4 splines bit: futile.logger: utils lambda.r futile.options pmp: stats impute pcaMethods missForest ggplot2 methods SummarizedExperiment S4Vectors matrixStats grDevices reshape2 utils RpsiXML: methods annotate graph Biobase RBGL XML hypergraph AnnotationDbi org.At.tair.db: methods AnnotationDbi Pi: igraph dnet ggplot2 graphics Matrix ggbio GenomicRanges GenomeInfoDb supraHex scales grDevices ggrepel ROCR randomForest glmnet Gviz lattice caret plot3D stats methods MASS IRanges BiocGenerics dplyr tidyr ggnetwork osfr RCircos purrr readr tibble iterativeBMAsurv: BMA leaps survival splines graphics grDevices stats utils DropletUtils: SingleCellExperiment utils stats methods Matrix Rcpp BiocGenerics S4Vectors SummarizedExperiment BiocParallel DelayedArray HDF5Array rhdf5 edgeR R.utils dqrng beachmat scuttle Rhdf5lib BH phastCons100way.UCSC.hg19: GenomicScores utils S4Vectors IRanges GenomicRanges GenomeInfoDb BSgenome interp: Rcpp deldir RcppEigen plethy: methods DBI RSQLite BiocGenerics S4Vectors Streamer IRanges reshape2 plyr RColorBrewer ggplot2 Biobase PWMEnrich.Mmusculus.background: methods PWMEnrich png: MultiAssayExperiment: SummarizedExperiment methods GenomicRanges BiocGenerics S4Vectors IRanges Biobase stats tidyr utils SELEX: rJava Biostrings stats utils mvoutData: methods Biobase affy lumi sgeostat: stats grDevices graphics loose.rock: digest futile.options ggplot2 graphics MASS methods httr dplyr reshape2 DiagrammeR: dplyr downloader glue htmltools htmlwidgets igraph influenceR magrittr purrr RColorBrewer readr rlang rstudioapi scales stringr tibble tidyr viridis visNetwork miRNAtap: AnnotationDbi DBI RSQLite stringr sqldf plyr methods covEB: mvtnorm igraph gsl Biobase stats LaplacesDemon Matrix registry: utils ebdbNet: igraph graphics stats HEM: Biobase grDevices stats utils git2r: graphics utils GenoGAM: SummarizedExperiment HDF5Array rhdf5 S4Vectors Matrix data.table Rcpp sparseinv Rsamtools GenomicRanges BiocParallel DESeq2 futile.logger GenomeInfoDb GenomicAlignments IRanges Biostrings DelayedArray methods stats RcppArmadillo VIM: colorspace grid car grDevices magrittr robustbase stats sp vcd MASS nnet e1071 methods Rcpp utils graphics laeken ranger data.table mhsmm: mvtnorm SEtools: S4Vectors SummarizedExperiment data.table pheatmap seriation ComplexHeatmap circlize methods BiocParallel randomcoloR edgeR openxlsx AnVIL: dplyr stats utils methods futile.logger jsonlite httr curl rapiclient tibble tidyselect rlang BiocManager changepoint: methods stats zoo formula.tools: operator.tools utils methods NanoStringDiff: Biobase matrixStats methods Rcpp runibic: biclust SummarizedExperiment Rcpp testthat methods stemHypoxia: cellranger: rematch tibble procoil: kebabs methods stats graphics S4Vectors Biostrings utils mstate: survival rlang data.table magrittr lattice RColorBrewer viridis SCOPE: GenomicRanges IRanges Rsamtools GenomeInfoDb BSgenome.Hsapiens.UCSC.hg19 stats grDevices graphics utils DescTools RColorBrewer gplots foreach parallel doParallel DNAcopy BSgenome Biostrings BiocGenerics S4Vectors karyoploteR: regioneR GenomicRanges methods IRanges Rsamtools stats graphics memoise rtracklayer GenomeInfoDb S4Vectors biovizBase digest bezier GenomicFeatures bamsignals AnnotationDbi grDevices VariantAnnotation CoRegNet: igraph shiny arules methods SemDist: AnnotationDbi GO.db annotate esetVis: mpm hexbin Rtsne MLP grid Biobase MASS stats utils grDevices methods ctgGEM: monocle SummarizedExperiment Biobase BiocGenerics graphics grDevices igraph methods utils sincell TSCAN destiny HSMMSingleCell xcms: methods Biobase BiocParallel MSnbase mzR BiocGenerics ProtGenerics lattice RColorBrewer plyr RANN MassSpecWavelet S4Vectors robustbase IRanges SummarizedExperiment MsCoreUtils qpdf: Rcpp askpass curl MEDIPS: BSgenome Rsamtools GenomicRanges Biostrings graphics gtools IRanges methods stats utils edgeR DNAcopy biomaRt rtracklayer preprocessCore sagenhaft: SparseM methods graphics stats utils RNAither: topGO RankProd prada geneplotter limma biomaRt car splots methods rapiclient: jsonlite httr yaml phastCons100way.UCSC.hg38: GenomicScores utils S4Vectors IRanges GenomicRanges GenomeInfoDb BSgenome mitools: DBI methods stats DOSE: AnnotationDbi BiocParallel DO.db fgsea ggplot2 GOSemSim methods qvalue reshape2 stats utils DaMiRseq: SummarizedExperiment ggplot2 DESeq2 limma EDASeq RColorBrewer sva Hmisc pheatmap FactoMineR corrplot randomForest e1071 caret MASS lubridate plsVarSel kknn FSelector methods stats utils graphics grDevices reshape2 ineq arm pls RSNNS edgeR plyr AMOUNTAIN: stats pogos: rjson httr methods S4Vectors utils shiny ontoProc ggplot2 graphics CellTrails: SingleCellExperiment BiocGenerics Biobase cba dendextend dtw EnvStats ggplot2 ggrepel grDevices igraph maptree methods mgcv reshape2 Rtsne stats splines SummarizedExperiment utils metavizr: metagenomeSeq methods data.table Biobase digest epivizr epivizrData epivizrServer epivizrStandalone vegan GenomeInfoDb phyloseq httr APAlyzer: GenomicRanges GenomicFeatures GenomicAlignments DESeq ggrepel SummarizedExperiment Rsubread stats ggplot2 methods rtracklayer ensembldb VariantAnnotation dplyr tidyr repmis exactRankTests: stats utils ggplotify: ggplot2 graphics grDevices grid gridGraphics rvcheck gespeR: methods graphics ggplot2 Matrix glmnet cellHTS2 Biobase biomaRt doParallel parallel foreach reshape2 dplyr FreqProf: reshape2 ggplot2 shiny longitudinalData: methods clv class rgl utils misc3d PADOG: KEGGdzPathwaysGEO methods Biobase limma AnnotationDbi GSA foreach doRNG hgu133plus2.db hgu133a.db KEGGREST nlme V8: Rcpp jsonlite curl utils stabledist: stats fftw: yarn: Biobase biomaRt downloader edgeR gplots graphics limma matrixStats preprocessCore readr RColorBrewer stats quantro pram: methods BiocParallel tools utils data.table GenomicAlignments rtracklayer BiocGenerics GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors OrgMassSpecR: grid ccmap: AnnotationDbi BiocManager ccdata doParallel data.table foreach parallel xgboost lsa DelayedDataFrame: S4Vectors DelayedArray methods stats BiocGenerics gprege: gptk PICS: utils stats graphics grDevices methods IRanges GenomicRanges Rsamtools GenomicAlignments mice: broom dplyr generics graphics lattice methods Rcpp rlang stats tidyr utils cpp11 InvariantCausalPrediction: glmnet mboost gCrisprTools: Biobase limma RobustRankAggreg ggplot2 PANTHER.db rmarkdown grDevices graphics stats utils parallel SummarizedExperiment GSEABenchmarkeR: Biobase SummarizedExperiment AnnotationDbi AnnotationHub BiocFileCache BiocParallel edgeR EnrichmentBrowser ExperimentHub grDevices graphics KEGGandMetacoreDzPathwaysGEO KEGGdzPathwaysGEO methods S4Vectors stats utils bmp: msdata: tximeta: SummarizedExperiment tximport jsonlite S4Vectors IRanges GenomicRanges AnnotationDbi GenomicFeatures ensembldb BiocFileCache AnnotationHub Biostrings tibble GenomeInfoDb rappdirs utils methods Matrix quadprog: qap: MiRaGE: Biobase BiocGenerics S4Vectors AnnotationDbi BiocManager aggregateBioVar: stats methods S4Vectors SummarizedExperiment SingleCellExperiment Matrix tibble rlang BSgenome.Rnorvegicus.UCSC.rn5: BSgenome BSgenome.Rnorvegicus.UCSC.rn6: BSgenome RWekajars: rJava genomewidesnp5Crlmm: utils maptpx: slam biscuiteer: biscuiteerData bsseq readr qualV Matrix impute HDF5Array S4Vectors Rsamtools data.table Biobase GenomicRanges BiocGenerics VariantAnnotation DelayedMatrixStats SummarizedExperiment GenomeInfoDb Mus.musculus Homo.sapiens matrixStats rtracklayer QDNAseq dmrseq methods utils R.utils gtools BiocParallel penalized: survival methods Rcpp RcppArmadillo CAnD: methods ggplot2 reshape RchyOptimyx: Rgraphviz sfsmisc graphics methods graph grDevices flowType flowTrans: flowCore flowViz flowClust methods stats AlphaBeta: dplyr data.table stringr utils gtools optimx expm stats BiocParallel igraph graphics ggplot2 grDevices plotly consensusSeekeR: BiocGenerics IRanges GenomicRanges BiocParallel GenomeInfoDb rtracklayer stringr S4Vectors methods DrugVsDisease: affy limma biomaRt ArrayExpress GEOquery DrugVsDiseasedata cMap2data qvalue annotate hgu133a.db hgu133a2.db hgu133plus2.db RUnit BiocGenerics xtable MMAPPR2: ensemblVEP gmapR Rsamtools VariantAnnotation BiocParallel Biobase BiocGenerics dplyr GenomeInfoDb GenomicRanges IRanges S4Vectors tidyr VariantTools magrittr methods grDevices graphics stats utils stringr data.table ARRmNormalization: ARRmData zFPKM: checkmate dplyr ggplot2 tidyr SummarizedExperiment googleAuthR: assertthat cli digest gargle httr jsonlite memoise rlang utils widyr: rlang dplyr tidyr reshape2 tidytext purrr Matrix broom REMP: SummarizedExperiment minfi readr rtracklayer graphics stats utils methods settings BiocGenerics S4Vectors Biostrings GenomicRanges IRanges GenomeInfoDb BiocParallel doParallel parallel foreach caret kernlab ranger BSgenome AnnotationHub org.Hs.eg.db impute iterators GOSim: GO.db annotate org.Hs.eg.db AnnotationDbi topGO cluster flexmix RBGL graph Matrix corpcor Rcpp DART: igraph csSAM: compiler pheatmap: grid RColorBrewer scales gtable stats grDevices graphics microbiome: phyloseq ggplot2 dplyr reshape2 Rtsne scales stats tibble tidyr utils vegan phylobase: ade4 ape Rcpp rncl grid methods stats RNeXML sampleClassifier: MGFM MGFR annotate e1071 ggplot2 stats utils chromswitch: GenomicRanges cluster Biobase BiocParallel dplyr gplots graphics grDevices IRanges lazyeval matrixStats magrittr methods NMF rtracklayer S4Vectors stats tidyr Rsubread: grDevices stats utils Matrix TnT: GenomicRanges methods stats utils grDevices htmlwidgets jsonlite data.table Biobase GenomeInfoDb IRanges S4Vectors knitr 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 iSEEu: iSEE methods S4Vectors shiny SummarizedExperiment SingleCellExperiment ggplot2 DT stats colourpicker splots: grid RColorBrewer made4: RColorBrewer gplots scatterplot3d Biobase SummarizedExperiment ade4 NewWave: SummarizedExperiment SharedObject methods SingleCellExperiment parallel irlba Matrix DelayedArray BiocSingular stats SmoothWin: nlme Rfast lionessR: stats SummarizedExperiment S4Vectors mockery: testthat R.rsp: methods stats tools utils R.methodsS3 R.oo R.utils R.cache digest RTCA: methods stats graphics Biobase RColorBrewer gtools ISoLDE: graphics grDevices stats utils gplots: gtools stats caTools KernSmooth methrix: data.table SummarizedExperiment rtracklayer DelayedArray HDF5Array BSgenome DelayedMatrixStats parallel methods ggplot2 matrixStats graphics stats utils GenomicRanges IRanges methimpute: GenomicRanges ggplot2 Rcpp methods utils grDevices stats GenomeInfoDb IRanges Biostrings reshape2 minpack.lm data.table ptw: nloptr graphics grDevices stats DuoClustering2018: ExperimentHub utils magrittr dplyr tidyr mclust ggplot2 purrr reshape2 viridis ggthemes stats methods BCRANK: methods Biostrings SISPA: genefilter GSVA changepoint data.table plyr ggplot2 DropletTestFiles: utils ExperimentHub AnnotationHub S4Vectors cba: grid proxy stats graphics grDevices methods flowBeads: methods Biobase rrcov flowCore knitr xtable Ringo: methods Biobase RColorBrewer limma Matrix grid lattice BiocGenerics genefilter vsn stats4 sigPathway: car: carData abind MASS mgcv nnet pbkrtest quantreg grDevices utils stats graphics maptools rio lme4 nlme HCAMatrixBrowser: AnVIL BiocFileCache digest dplyr httr jsonlite Matrix methods progress rlang SingleCellExperiment stats utils logspline: stats graphics transomics2cytoscape: RCy3 KEGGREST dplyr SigsPack: quadprog methods Biobase BSgenome VariantAnnotation Biostrings GenomeInfoDb GenomicRanges rtracklayer SummarizedExperiment graphics stats utils flowVS: methods flowCore flowViz flowStats HumanTranscriptomeCompendium: shiny ssrch S4Vectors SummarizedExperiment utils rintrojs: shiny jsonlite phantasus: ggplot2 protolite Biobase GEOquery Rook htmltools httpuv jsonlite limma opencpu assertthat methods httr rhdf5 utils parallel stringr fgsea svglite gtable stats Matrix pheatmap scales ccaPP grid grDevices AnnotationDbi DESeq2 curl SCLCBam: multiMiR: stats XML RCurl purrr tibble methods BiocGenerics AnnotationDbi dplyr pepDat: GenomicRanges phenoTest: Biobase methods annotate Heatplus BMA ggplot2 Hmisc survival limma gplots Category AnnotationDbi hopach biomaRt GSEABase genefilter xtable mgcv hgu133a.db ellipse BRAIN: PolynomF Biostrings lattice CompGO: RDAVIDWebService rtracklayer Rgraphviz ggplot2 GenomicFeatures TxDb.Mmusculus.UCSC.mm9.knownGene pcaMethods reshape2 pathview BSgenome.Mmusculus.UCSC.mm8.masked: BSgenome BSgenome.Mmusculus.UCSC.mm8 drawProteins: ggplot2 httr dplyr readr tidyr rGADEM: Biostrings IRanges BSgenome methods seqLogo GenomicRanges graphics ClueR: e1071 parallel ChAMPdata: GenomicRanges BiocGenerics multtest: methods BiocGenerics Biobase survival MASS stats4 ceRNAnetsim: dplyr tidygraph furrr rlang tibble ggplot2 ggraph igraph purrr tidyr future stats decontam: methods ggplot2 reshape2 stats RTCGA.CNV: RTCGA Matching: MASS graphics grDevices stats SCATE: parallel preprocessCore splines splines2 xgboost SCATEData Rtsne mclust utils stats GenomicAlignments GenomicRanges scone: methods SummarizedExperiment graphics stats utils aroma.light BiocParallel class cluster compositions diptest edgeR fpc gplots grDevices hexbin limma matrixStats mixtools RColorBrewer boot rhdf5 RUVSeq rARPACK CrossICC: MASS data.table methods MergeMaid ConsensusClusterPlus limma cluster dplyr Biobase grDevices stats graphics utils methyAnalysis: grid BiocGenerics IRanges GenomeInfoDb GenomicRanges Biobase org.Hs.eg.db grDevices stats utils lumi methylumi Gviz genoset SummarizedExperiment VariantAnnotation rtracklayer bigmemoryExtras GenomicFeatures annotate AnnotationDbi genefilter biomaRt methods parallel BSgenome.Mmusculus.UCSC.mm9.masked: BSgenome BSgenome.Mmusculus.UCSC.mm9 isobar: Biobase stats methods distr plyr biomaRt ggplot2 rebook: utils methods knitr callr rmarkdown CodeDepends BiocStyle ReactomeGSA: jsonlite httr progress ggplot2 methods gplots RColorBrewer pwr: stats graphics spatstat.sparse: stats utils methods Matrix abind tensor spatstat.utils ADImpute: ArgumentCheck BiocParallel data.table DrImpute kernlab MASS Matrix methods rsvd S4Vectors SAVER SingleCellExperiment stats SummarizedExperiment utils affyio: zlibbioc methods PhosR: ruv e1071 calibrate dendextend limma pcaMethods stats RColorBrewer circlize dplyr igraph pheatmap preprocessCore tidyr rlang graphics grDevices utils glmnetUtils: stats graphics grDevices glmnet parallel Matrix padma: SummarizedExperiment S4Vectors FactoMineR MultiAssayExperiment methods graphics stats utils densvis: Rcpp basilisk assertthat reticulate deltaCaptureC: IRanges GenomicRanges SummarizedExperiment ggplot2 DESeq2 pkgmaker: methods stats registry tools grDevices utils graphics codetools digest stringr xtable withr assertthat MSstatsSampleSize: ggplot2 BiocParallel caret gridExtra reshape2 stats utils grDevices graphics MSstats splines: graphics stats sangerseqR: Biostrings methods shiny sROC: RTCGA.PANCAN12: RTCGA carData: chron: graphics stats RUVSeq: Biobase EDASeq edgeR methods MASS ncRNAtools: httr xml2 utils methods grDevices ggplot2 IRanges GenomicRanges S4Vectors IVAS: GenomicFeatures ggplot2 Biobase doParallel lme4 BiocGenerics GenomicRanges IRanges foreach AnnotationDbi S4Vectors GenomeInfoDb ggfortify grDevices methods Matrix BiocParallel utils stats fastICA: logicFS: LogicReg mcbiopi survival graphics methods stats gRain: methods gRbase graph Rgraphviz igraph stats4 magrittr Rcpp RcppArmadillo RcppEigen GeneTonic: AnnotationDbi bs4Dash colorspace ComplexHeatmap dendextend DESeq2 dplyr DT dynamicTreeCut expm ggforce ggplot2 ggrepel GO.db graphics grDevices grid igraph matrixStats methods plotly RColorBrewer rintrojs rlang rmarkdown S4Vectors scales shiny shinycssloaders shinyWidgets stats SummarizedExperiment tidyr tools utils viridis visNetwork uwot: Matrix Rcpp methods FNN RSpectra RcppAnnoy irlba RcppProgress dqrng CiteFuse: SingleCellExperiment SummarizedExperiment Matrix mixtools cowplot ggplot2 gridExtra grid dbscan propr uwot Rtsne S4Vectors igraph scales scran graphics methods stats utils reshape2 ggridges randomForest pheatmap ggraph grDevices rhdf5 rlang CoGAPS: BiocParallel cluster methods gplots graphics grDevices RColorBrewer Rcpp S4Vectors SingleCellExperiment stats SummarizedExperiment tools utils rhdf5 dendsort: future.apply: future globals parallel utils RITAN: graphics stats utils grid gridExtra reshape2 gplots ggplot2 plotrix RColorBrewer STRINGdb MCL linkcomm dynamicTreeCut gsubfn hash png sqldf igraph BgeeDB knitr RITANdata fdrame: tcltk graphics grDevices stats utils ExpressionAtlas: methods Biobase SummarizedExperiment limma S4Vectors xml2 utils XML httr network: utils tibble magrittr XINA: mclust plyr alluvial ggplot2 igraph gridExtra tools grDevices graphics utils STRINGdb roar: methods BiocGenerics S4Vectors IRanges GenomicRanges SummarizedExperiment GenomicAlignments rtracklayer GenomeInfoDb rversions: curl utils xml2 cliqueMS: Rcpp xcms MSnbase igraph qlcMatrix matrixStats methods BH RcppArmadillo kinship2: Matrix quadprog graphics stats methods GetoptLong: rjson GlobalOptions methods crayon TxDb.Drerio.UCSC.danRer10.refGene: GenomicFeatures AnnotationDbi mogsa: methods graphite genefilter BiocGenerics gplots GSEABase Biobase parallel corpcor svd cluster grDevices graphics stats utils DegNorm: methods Rcpp GenomicFeatures parallel foreach S4Vectors doParallel Rsamtools GenomicAlignments heatmaply data.table stats ggplot2 GenomicRanges IRanges plyr plotly utils viridis RcppArmadillo beadarray: BiocGenerics Biobase hexbin BeadDataPackR limma AnnotationDbi stats4 reshape2 GenomicRanges IRanges illuminaio methods ggplot2 tidyr: dplyr ellipsis glue lifecycle magrittr purrr rlang tibble tidyselect utils vctrs cpp11 affyPara: methods affy snow vsn aplpack affyio biscuiteerData: ExperimentHub AnnotationHub utils curl dpeak: methods stats utils graphics Rcpp MASS IRanges BSgenome grDevices parallel TTMap: rgl colorRamps grDevices graphics stats utils methods SummarizedExperiment Biobase clst: ROC lattice systemPipeShiny: shiny spsUtil spsComps drawer DT assertthat bsplus crayon dplyr ggplot2 glue magrittr methods plotly rlang rstudioapi shinyAce shinyFiles shinyWidgets shinydashboard shinydashboardPlus shinyjqui shinyjs shinytoastr stringr stats styler tibble utils vroom yaml RNASeqRData: tidyverse: broom cli crayon dbplyr dplyr dtplyr forcats googledrive googlesheets4 ggplot2 haven hms httr jsonlite lubridate magrittr modelr pillar purrr readr readxl reprex rlang rstudioapi rvest stringr tibble tidyr xml2 bit64: bit utils methods stats MetaCycle: gnm fftwtools: gert: askpass credentials openssl rstudioapi sys zip sigFeature: biocViews nlme e1071 openxlsx pheatmap RColorBrewer Matrix SparseM graphics stats utils SummarizedExperiment BiocParallel methods ORCME: Iso graph: methods BiocGenerics stats stats4 utils RcppParallel: rainbow: MASS pcaPP hdrcde cluster colorspace ks cytolib: RcppParallel RProtoBufLib Rcpp BH Rhdf5lib RcppArmadillo mime: tools NMFN: base64url: backports consensus: RColorBrewer matrixStats gplots grDevices methods graphics stats utils imputeLCMD: tmvtnorm norm pcaMethods impute MOFAdata: R.cache: utils R.methodsS3 R.oo R.utils digest PING: methods PICS graphics grDevices stats Gviz fda BSgenome stats4 BiocGenerics IRanges GenomicRanges S4Vectors kmer: openssl phylogram Rcpp cp4p: MESS graphics stats multtest qvalue limma a4: a4Base a4Preproc a4Classif a4Core a4Reporting ggpmisc: ggplot2 grid rlang magrittr generics glue gridExtra scales MASS polynom splus2R tibble plyr dplyr xts zoo lubridate stringr MicrobiotaProcess: ape plyr tidyr ggplot2 phyloseq magrittr dplyr Biostrings ggrepel vegan reshape zoo ggtree tidytree gtools MASS methods rlang tibble grDevices stats utils coin ggsignif Rmisc patchwork ggstar dunn.test: pcxn: pcxnData methods grDevices utils pheatmap splancs: sp stats graphics grDevices methods clue: stats cluster graphics methods MLmetrics: stats utils ROCR TxDb.Celegans.UCSC.ce6.ensGene: GenomicFeatures AnnotationDbi fission: SummarizedExperiment glmnet: Matrix methods utils foreach shape survival marray: limma methods MODA: grDevices graphics stats utils WGCNA dynamicTreeCut igraph cluster AMOUNTAIN RColorBrewer customProDB: IRanges AnnotationDbi biomaRt S4Vectors DBI GenomeInfoDb GenomicRanges Rsamtools GenomicAlignments Biostrings GenomicFeatures stringr RCurl plyr VariantAnnotation rtracklayer RSQLite AhoCorasickTrie methods topdownr: methods BiocGenerics ProtGenerics Biostrings S4Vectors grDevices stats tools utils Biobase Matrix MSnbase ggplot2 mzR ENCODExplorerData: tools jsonlite RCurl data.table methods commonmark: QuartPAC: iPAC GraphPAC SpacePAC data.table printr: knitr KOdata: CancerMutationAnalysis: qvalue AnnotationDbi limma methods stats gwasurvivr: GWASTools survival VariantAnnotation parallel matrixStats SummarizedExperiment stats utils SNPRelate RNAmodR.Data: ExperimentHub ExperimentHubData utils Rmixmod: Rcpp methods RcppEigen joda: bgmm RBGL ICS: methods mvtnorm survey graphics flowCHIC: methods flowCore EBImage vegan hexbin ggplot2 grid party: methods grid stats mvtnorm modeltools strucchange survival coin zoo sandwich magick: Rcpp magrittr curl Rhtslib: zlibbioc ffbase: ff fastmatch bit MafDb.1Kgenomes.phase1.hs37d5: GenomicScores utils S4Vectors IRanges GenomicRanges GenomeInfoDb BSgenome rvcheck: BiocManager utils rlang org.Sc.sgd.db: methods AnnotationDbi tweedie: scRNAseq: SingleCellExperiment utils methods BiocGenerics S4Vectors GenomicRanges SummarizedExperiment ExperimentHub AnnotationHub AnnotationDbi ensembldb GenomicFeatures CDFt: stats pandaR: methods Biobase BiocGenerics matrixStats igraph ggplot2 grid reshape plyr RUnit hexbin bdsmatrix: methods RCy3: httr methods RJSONIO XML utils BiocGenerics igraph stats graph R.utils minerva: parallel Rcpp stats graphics RcppArmadillo segmented: linprog: lpSolve StructuralVariantAnnotation: GenomicRanges rtracklayer VariantAnnotation BiocGenerics assertthat Biostrings stringr dplyr methods rlang Herper: reticulate utils rjson withr stats TDARACNE: GenKern Rgraphviz Biobase MOFA: rhdf5 dplyr reshape2 pheatmap corrplot ggplot2 ggbeeswarm methods scales GGally RColorBrewer cowplot ggrepel MultiAssayExperiment Biobase doParallel foreach reticulate grDevices stats utils pinfsc50: ImpulseDE: graphics grDevices stats utils parallel compiler amap boot sRACIPE: SummarizedExperiment methods Rcpp ggplot2 reshape2 MASS RColorBrewer gridExtra visNetwork gplots umap htmlwidgets S4Vectors BiocGenerics grDevices stats utils graphics hiAnnotator: GenomicRanges foreach iterators rtracklayer dplyr BSgenome ggplot2 scales methods clisymbols: BSgenome: methods BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges Biostrings rtracklayer utils stats matrixStats XVector Rsamtools sparsesvd: Matrix methods SynExtend: DECIPHER igraph methods Biostrings S4Vectors IRanges utils stats withr: graphics grDevices stats hgu95av2.db: methods AnnotationDbi org.Hs.eg.db optparse: methods getopt npGSEA: GSEABase Biobase methods BiocGenerics graphics stats RImmPort: plyr dplyr DBI data.table reshape2 methods sqldf tools utils RSQLite FSelector: digest entropy randomForest RWeka seq2pathway: nnet WGCNA GSA biomaRt GenomicRanges seq2pathway.data haplo.stats: methods stats graphics arsenal rms PROcess: Icens graphics grDevices stats utils MafDb.1Kgenomes.phase3.hs37d5: GenomicScores utils S4Vectors IRanges GenomicRanges GenomeInfoDb BSgenome debCAM: methods rJava BiocParallel stats Biobase SummarizedExperiment corpcor geometry NMF nnls DMwR pcaPP apcluster graphics SCnorm: SingleCellExperiment SummarizedExperiment stats methods graphics grDevices parallel quantreg cluster moments data.table BiocParallel S4Vectors ggplot2 forcats BiocGenerics annmap: methods GenomicRanges DBI RMySQL digest Biobase grid lattice Rsamtools genefilter IRanges BiocGenerics av: graphics SpectralTAD: dplyr PRIMME cluster Matrix parallel BiocParallel magrittr HiCcompare GenomicRanges SummarizedExperiment: methods MatrixGenerics GenomicRanges Biobase utils stats tools Matrix BiocGenerics S4Vectors IRanges GenomeInfoDb DelayedArray transcriptogramer: methods biomaRt data.table doSNOW foreach ggplot2 graphics grDevices igraph limma parallel progress RedeR snow stats tidyr topGO fontBitstreamVera: influenceR: igraph Matrix methods utils rTRM: igraph AnnotationDbi DBI RSQLite MSstatsQCgui: shiny MSstatsQC ggExtra gridExtra plotly dplyr grid TSCAN: ggplot2 shiny plyr grid fastICA igraph combinat mgcv mclust gplots methods stats Matrix SummarizedExperiment SingleCellExperiment DelayedArray S4Vectors cli: glue utils Illumina450ProbeVariants.db: RITANdata: downloader: utils digest PathoStat: limma corpcor matrixStats reshape2 scales ggplot2 rentrez DT tidyr plyr dplyr phyloseq shiny stats methods XML graphics utils BiocStyle edgeR DESeq2 ComplexHeatmap plotly webshot vegan shinyjs glmnet gmodels ROCR RColorBrewer knitr devtools ape struct: methods ontologyIndex datasets graphics stats utils knitr SummarizedExperiment S4Vectors pcalg: stats graphics utils methods abind graph RBGL igraph ggm corpcor robustbase vcd Rcpp bdsmatrix sfsmisc fastICA clue RcppArmadillo BH ca: ABAData: tkWidgets: methods widgetTools DynDoc tools EBcoexpress: EBarrays mclust minqa scater: SingleCellExperiment ggplot2 stats utils methods grid gridExtra Matrix BiocGenerics S4Vectors SummarizedExperiment DelayedArray DelayedMatrixStats BiocNeighbors BiocSingular BiocParallel scuttle rlang ggbeeswarm viridis VennDetail: utils grDevices stats methods dplyr purrr tibble magrittr ggplot2 UpSetR VennDiagram grid futile.logger rrcov: robustbase methods stats stats4 mvtnorm lattice pcaPP WGSmapp: GenomicRanges clv: cluster class BiocParallel: methods stats utils futile.logger parallel snow BH missForest: randomForest foreach itertools CAGEfightR: GenomicRanges rtracklayer SummarizedExperiment pryr assertthat methods Matrix BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicFeatures GenomicAlignments BiocParallel GenomicFiles Gviz InteractionSet GenomicInteractions RGMQLlib: assertive.sets: assertive.base AffiXcan: SummarizedExperiment MultiAssayExperiment BiocParallel crayon pcot2: grDevices Biobase amap ITALICSData: BiocSklearn: reticulate methods SummarizedExperiment knitr basilisk Rcpp wateRmelon: Biobase limma methods matrixStats methylumi lumi ROC IlluminaHumanMethylation450kanno.ilmn12.hg19 illuminaio intansv: plyr ggbio GenomicRanges BiocGenerics IRanges mzID: methods XML plyr parallel doParallel foreach iterators ProtGenerics RSVSim: Biostrings GenomicRanges methods IRanges ShortRead ELMER: ELMER.data GenomicRanges ggplot2 reshape grid grDevices graphics methods parallel stats utils IRanges GenomeInfoDb S4Vectors GenomicFeatures TCGAbiolinks plyr Matrix dplyr Gviz ComplexHeatmap circlize MultiAssayExperiment SummarizedExperiment biomaRt doParallel downloader ggrepel lattice magrittr readr scales rvest xml2 plotly gridExtra rmarkdown stringr tibble tidyr progress purrr reshape2 ggpubr rtracklayer DelayedArray ccaPP: parallel pcaPP robustbase Rcpp RcppArmadillo TxDb.Dmelanogaster.UCSC.dm3.ensGene: GenomicFeatures AnnotationDbi R.huge: R.methodsS3 R.oo R.utils eisa: isa2 Biobase AnnotationDbi methods BiocGenerics Category genefilter DBI IHW: methods slam lpsymphony fdrtool BiocGenerics GreyListChIP: methods GenomicRanges GenomicAlignments BSgenome Rsamtools rtracklayer MASS parallel GenomeInfoDb SummarizedExperiment stats utils circlize: graphics GlobalOptions shape grDevices utils stats colorspace methods grid reactR: htmltools broom: backports dplyr ellipsis generics glue methods purrr rlang stringr tibble tidyr rhandsontable: jsonlite htmlwidgets magrittr methods GeneRegionScan: methods Biobase Biostrings S4Vectors affxparser RColorBrewer RnBeads: BiocGenerics S4Vectors GenomicRanges MASS cluster ff fields ggplot2 gplots gridExtra limma matrixStats methods illuminaio methylumi plyr IRanges CSAR: S4Vectors IRanges GenomeInfoDb GenomicRanges stats utils cycle: Mfuzz Biobase stats ragg: systemfonts textshaping pscl: MASS datasets grDevices graphics stats utils CGHnormaliter: CGHcall CGHbase Biobase methods stats utils CluMSID: mzR S4Vectors dbscan RColorBrewer ape network GGally ggplot2 plotly methods utils stats sna grDevices graphics Biobase gplots MSnbase ROntoTools: methods graph boot KEGGREST KEGGgraph Rgraphviz StanHeaders: RcppParallel RcppEigen GLAD: aws animation: magick RSpectra: Matrix Rcpp RcppEigen scGPS: SummarizedExperiment dynamicTreeCut SingleCellExperiment glmnet caret ggplot2 fastcluster dplyr Rcpp RcppArmadillo RcppParallel grDevices graphics stats utils DESeq locfit CATALYST: SingleCellExperiment circlize ComplexHeatmap ConsensusClusterPlus cowplot data.table dplyr drc flowCore FlowSOM ggplot2 ggrepel ggridges graphics grDevices grid gridExtra magrittr Matrix matrixStats methods nnls purrr RColorBrewer reshape2 Rtsne SummarizedExperiment S4Vectors scales scater stats bsseqData: bsseq pvclust: normalize450K: Biobase illuminaio quadprog utils RobustRankAggreg: methods sigsquared: methods Biobase survival CoRegFlux: CoRegNet sybil attempt: rlang ff: bit utils curatedBladderData: affy RCyjs: BrowserViz graph methods httpuv BiocGenerics base64enc utils pander: grDevices graphics methods utils stats digest tools Rcpp ppclust: graphics grDevices inaparc MASS stats utils methods MetNet: bnlearn BiocParallel GENIE3 methods mpmi parmigene ppcor sna stabs stats PathNet: OmicsLonDA: SummarizedExperiment gss plyr zoo pracma ggplot2 BiocParallel parallel grDevices graphics stats utils methods BiocGenerics HSMMSingleCell: genbankr: methods BiocGenerics IRanges GenomicRanges GenomicFeatures Biostrings VariantAnnotation rtracklayer S4Vectors GenomeInfoDb Biobase gQTLBase: GenomicRanges methods BatchJobs BBmisc S4Vectors BiocGenerics foreach doParallel bit ff rtracklayer ffbase GenomicFiles SummarizedExperiment gamlss: graphics stats splines utils grDevices gamlss.data gamlss.dist nlme parallel MASS survival methods Rdpack: methods tools utils rbibutils BufferedMatrixMethods: BufferedMatrix methods leiden: methods reticulate Matrix igraph rnaSeqMap: methods Biobase Rsamtools GenomicAlignments GenomicRanges IRanges edgeR DESeq DBI fs: methods qtl: parallel graphics stats utils grDevices waffle: ggplot2 RColorBrewer grid gridExtra gtable extrafont RFOC: RPMG GEOmap RSEIS MASS splancs gh: cli gitcreds httr ini jsonlite iClusterPlus: parallel maser: ggplot2 GenomicRanges dplyr rtracklayer reshape2 Gviz DT GenomeInfoDb stats utils IRanges methods BiocGenerics parallel data.table knitr: evaluate highr methods markdown stringr yaml xfun tools breastCancerUNT: reb: Biobase idiogram missRows: methods ggplot2 grDevices MultiAssayExperiment plyr stats gtools S4Vectors rols: methods httr progress jsonlite utils Biobase BiocGenerics bigmelon: wateRmelon gdsfmt methods minfi Biobase methylumi stats utils GEOquery graphics BiocGenerics fCI: FNN psych gtools zoo rgl grid VennDiagram MOMA: circlize cluster ComplexHeatmap dplyr ggplot2 graphics grid grDevices magrittr methods MKmisc MultiAssayExperiment parallel qvalue RColorBrewer readr reshape2 rlang stats stringr tibble tidyr utils cTRAP: biomaRt binr cowplot data.table dplyr DT fgsea ggplot2 ggrepel graphics highcharter httr limma methods pbapply R.utils readxl reshape2 rhdf5 scales shiny stats tools utils restfulSEData: SummarizedExperiment ExperimentHub utils methods tagcloud: Rcpp RColorBrewer GenomicScores: S4Vectors GenomicRanges methods BiocGenerics stats utils XML Biobase BiocManager BiocFileCache IRanges Biostrings GenomeInfoDb AnnotationHub rhdf5 DelayedArray HDF5Array cqn: mclust nor1mix stats preprocessCore splines quantreg rain: gmp multtest argparser: methods reader: utils NCmisc grDevices graphics stats methods GOpro: AnnotationDbi dendextend doParallel foreach parallel org.Hs.eg.db GO.db Rcpp stats graphics MultiAssayExperiment IRanges S4Vectors BH Exact: graphics stats rootSolve interactiveDisplay: methods BiocGenerics grid interactiveDisplayBase shiny RColorBrewer ggplot2 reshape2 plyr gridSVG XML Category AnnotationDbi acde: boot stats graphics dada2: Rcpp methods Biostrings ggplot2 reshape2 ShortRead RcppParallel parallel IRanges XVector BiocGenerics MAIT: CAMERA Rcpp pls gplots e1071 class MASS plsgenomics agricolae xcms methods caret CFAssay: genomation: grid Biostrings BSgenome data.table GenomeInfoDb GenomicRanges GenomicAlignments S4Vectors ggplot2 gridBase impute IRanges matrixStats methods parallel plotrix plyr readr reshape2 Rsamtools seqPattern rtracklayer RUnit Rcpp scDblFinder: igraph Matrix BiocGenerics BiocParallel BiocNeighbors BiocSingular S4Vectors SummarizedExperiment SingleCellExperiment scran scater scuttle bluster methods DelayedArray xgboost stats utils BSgenome.Rnorvegicus.UCSC.rn5.masked: BSgenome BSgenome.Rnorvegicus.UCSC.rn5 cmdfun: magrittr purrr R.utils rlang testthat usethis utils cairoDevice: grDevices flowMap: ade4 doParallel abind reshape2 scales Matrix methods rex: lazyeval AMARETTO: impute doParallel grDevices dplyr methods ComplexHeatmap callr Matrix Rcpp BiocFileCache DT MultiAssayExperiment circlize curatedTCGAData foreach glmnet httr limma matrixStats readr reshape2 tibble rmarkdown graphics grid parallel stats knitr ggplot2 gridExtra utils tfruns: utils jsonlite base64enc yaml config magrittr whisker tidyselect rlang rstudioapi reticulate geuvStore2: BatchJobs GenomicRanges methods gQTLBase rSWeeP: pracma stats PRROC: sparsenetgls: Matrix MASS methods glmnet huge stats graphics utils gRbase: methods graph Rgraphviz RBGL stats4 igraph magrittr Matrix Rcpp RcppEigen RcppArmadillo peco: assertthat circular conicfit doParallel foreach genlasso graphics methods parallel scater SingleCellExperiment SummarizedExperiment stats utils intergraph: network igraph utils metaboliteIDmapping: AnnotationHub fastLiquidAssociation: methods LiquidAssociation parallel doParallel stats Hmisc utils WGCNA impute preprocessCore NetSAM: methods igraph seriation graph rootSolve: stats graphics grDevices Mergeomics: rgl: graphics grDevices stats utils htmlwidgets htmltools knitr jsonlite shiny magrittr crosstalk manipulateWidget ctc: amap dexus: methods BiocGenerics stats timecourse: MASS methods Biobase graphics limma marray stats webbioc: Biobase affy multtest annaffy vsn gcrma qvalue stats utils BiocManager MotIV: graphics BiocGenerics GenomicRanges methods stats grid S4Vectors IRanges Biostrings lattice rGADEM utils ggnetwork: ggplot2 ggrepel network igraph sna utils DiscoRhythm: matrixTests matrixStats MetaCycle data.table ggplot2 ggExtra dplyr broom shiny shinyBS shinycssloaders shinydashboard shinyjs BiocStyle rmarkdown knitr kableExtra magick VennDiagram UpSetR heatmaply viridis plotly DT gridExtra methods stats SummarizedExperiment BiocGenerics S4Vectors zip reshape2 NbClust: maqcExpression4plex: rama: MethylMix: foreach RPMM RColorBrewer ggplot2 RCurl impute data.table limma R.matlab digest TBX20BamSubset: Rsamtools xtable cydar: SingleCellExperiment viridis methods shiny graphics stats grDevices utils BiocGenerics S4Vectors BiocParallel SummarizedExperiment flowCore Biobase Rcpp BiocNeighbors BADER: perturbatr: methods stats dplyr ggplot2 tidyr assertthat lme4 splines igraph foreach parallel doParallel diffusr lazyeval tibble grid utils graphics scales magrittr formula.tools rlang MafDb.gnomADex.r2.1.hs37d5: GenomicScores utils S4Vectors IRanges GenomicRanges GenomeInfoDb BSgenome illuminaHumanv1.db: methods AnnotationDbi org.Hs.eg.db s4vd: biclust methods irlba foreach lydata: MeSH.AOR.db: MeSHDbi pryr: stringr codetools methods Rcpp fields: methods spam maps alpine: Biostrings IRanges GenomicRanges GenomicAlignments Rsamtools SummarizedExperiment GenomicFeatures speedglm splines graph RBGL stringr stats methods graphics GenomeInfoDb S4Vectors XDE: Biobase BiocGenerics genefilter graphics grDevices gtools methods stats utils mvtnorm RColorBrewer GeneMeta siggenes ks: FNN kernlab KernSmooth Matrix mclust mgcv multicool mvtnorm plot3D MeSHDbi: BiocGenerics methods AnnotationDbi RSQLite Biobase RMariaDB: bit64 DBI hms lubridate methods Rcpp plogr rio: tools stats utils foreign haven curl data.table readxl openxlsx tibble IPO: xcms rsm CAMERA grDevices graphics stats utils BiocParallel aroma.affymetrix: R.utils aroma.core methods R.methodsS3 R.oo R.cache R.devices R.filesets aroma.apd MASS splines matrixStats listenv future stabs: methods stats parallel graphics grDevices utils AnVILPublish: AnVIL httr rmarkdown whisker tools utils stats processx: ps R6 utils nsprcomp: stats hu6800.db: methods AnnotationDbi org.Hs.eg.db getopt: stats fontquiver: fontBitstreamVera fontLiberation boot: graphics stats pd.hg.u95a: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors rsbml: BiocGenerics methods utils graph epivizr: methods epivizrServer epivizrData GenomicRanges S4Vectors IRanges bumphunter GenomeInfoDb BiocDockerManager: httr whisker readr dplyr utils methods memoise OLIN: methods locfit marray graphics grDevices limma stats deltaGseg: methods ggplot2 changepoint wavethresh tseries pvclust fBasics grid reshape scales bsplus: htmltools magrittr purrr lubridate stringr rmarkdown methods glue jsonlite coMET: grid utils biomaRt Gviz psych colortools hash grDevices gridExtra rtracklayer IRanges S4Vectors GenomicRanges stats corrplot MuMIn: graphics methods Matrix stats stats4 nlme PSCBS: utils R.methodsS3 R.oo R.utils R.cache matrixStats aroma.light DNAcopy listenv future parallel leukemiasEset: Biobase plasFIA: proFIA ggiraph: grid ggplot2 htmlwidgets stats htmltools Rcpp gdtools purrr rlang uuid pd.hg.u95av2: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors learnr: utils parallel withr rappdirs rprojroot jsonlite htmltools htmlwidgets evaluate knitr markdown shiny rmarkdown ellipsis checkmate renv MACSQuantifyR: readxl graphics tools utils grDevices ggplot2 ggrepel methods stats latticeExtra lattice rmarkdown png grid gridExtra prettydoc rvest xml2 chipenrich.data: AnnotationDbi BiocGenerics methods GenomicRanges GenomeInfoDb IRanges readr rtracklayer S4Vectors utils maxstat: exactRankTests mvtnorm stats graphics shinyAce: shiny jsonlite utils tools extraDistr: Rcpp polspline: stats graphics GA4GHshiny: GA4GHclient AnnotationDbi BiocGenerics dplyr DT GenomeInfoDb openxlsx GenomicFeatures methods purrr S4Vectors shiny shinyjs tidyr shinythemes tidySummarizedExperiment: SummarizedExperiment tibble dplyr magrittr tidyr ggplot2 rlang purrr lifecycle methods plotly utils S4Vectors tidyselect ellipsis pillar stringr cli fansi AffyRNADegradation: methods affy spatial: graphics stats utils AneuFinderData: HiCDataHumanIMR90: rle: methods tester: DEGreport: utils methods Biobase BiocGenerics broom circlize ComplexHeatmap cowplot ConsensusClusterPlus cluster DESeq2 dplyr edgeR ggplot2 ggdendro grid ggrepel grDevices knitr logging lasso2 magrittr Nozzle.R1 psych RColorBrewer reshape rlang scales stats stringr S4Vectors SummarizedExperiment tidyr tibble TFMPvalue: Rcpp MatrixRider: methods TFBSTools IRanges XVector Biostrings S4Vectors Rook: utils tools methods brew diffloop: methods GenomicRanges foreach plyr dplyr reshape2 ggplot2 matrixStats Sushi edgeR locfit statmod biomaRt GenomeInfoDb S4Vectors IRanges grDevices graphics stats utils Biobase readr data.table rtracklayer pbapply limma expm: Matrix methods np: boot cubature methods quadprog quantreg stats bacon: methods stats ggplot2 graphics BiocParallel ellipse c3net: igraph pathwayPCA: lars methods parallel stats survival utils numbers: shinyWidgets: bslib sass shiny htmltools jsonlite grDevices rafalib: RColorBrewer matchBox: nanotatoR: hash openxlsx rentrez stats grDevices graphics stringr knitr testthat utils AnnotationDbi httr org.Hs.eg.db rtracklayer laeken: boot MASS GWASTools: Biobase graphics stats utils methods gdsfmt DBI RSQLite GWASExactHW DNAcopy survival sandwich lmtest logistf quantsmooth data.table caret: lattice ggplot2 foreach methods plyr ModelMetrics nlme reshape2 stats stats4 utils grDevices recipes withr pROC mirna10cdf: utils AnnotationDbi NBAMSeq: SummarizedExperiment S4Vectors DESeq2 mgcv BiocParallel genefilter methods stats rhdf5filters: Rhdf5lib qusage: limma methods utils Biobase nlme emmeans fftw rae230aprobe: AnnotationDbi target: BiocGenerics GenomicRanges IRanges matrixStats methods stats graphics shiny celestial: RANN NISTunits pracma sitmo: Rcpp bpca: scatterplot3d rgl xtable ggvis: assertthat jsonlite shiny magrittr dplyr rlang htmltools methods muStat: stats awsMethods: methods SDAMS: SummarizedExperiment trust qvalue methods stats utils farms: affy MASS methods Biobase graphics CNORfeeder: CellNOptR graph TxDb.Mmusculus.UCSC.mm10.ensGene: GenomicFeatures AnnotationDbi ggplot.multistats: methods rlang scales hexbin ggplot2 pbmcapply: utils parallel RDAVIDWebService: methods graph GOstats ggplot2 Category GO.db RBGL rJava TimeSeriesExperiment: S4Vectors SummarizedExperiment dynamicTreeCut dplyr edgeR DESeq2 ggplot2 graphics Hmisc limma methods magrittr proxy stats tibble tidyr vegan viridis utils SynMut: seqinr methods Biostrings stringr BiocGenerics QDNAseq.mm10: QDNAseq SparseDC: stats rms: Hmisc survival lattice ggplot2 SparseM methods quantreg rpart nlme polspline multcomp htmlTable htmltools MASS cluster digest tictoc: methods org.Dm.eg.db: methods AnnotationDbi SSPA: methods graphics stats qvalue lattice limma HTSFilter: edgeR DESeq2 BiocParallel Biobase utils stats grDevices graphics methods MPFE: Biostrings: methods BiocGenerics S4Vectors IRanges XVector utils grDevices graphics stats crayon fcoex: FCBF parallel progress dplyr ggplot2 ggrepel igraph grid intergraph stringr clusterProfiler data.table grDevices methods network scales sna utils stats SingleCellExperiment pathwayPCA jpeg: beanplot: ps: utils gsubfn: proto nnNorm: marray graphics grDevices methods nnet stats sparsebn: sparsebnUtils ccdrAlgorithm discretecdAlgorithm epivizrStandalone: epivizr methods git2r epivizrServer GenomeInfoDb BiocGenerics GenomicFeatures S4Vectors geigen: MBCB: tcltk tcltk2 preprocessCore stats utils parglms: methods BiocGenerics BatchJobs foreach doParallel hgu133atagprobe: AnnotationDbi sparseMVN: Matrix methods deSolve: methods graphics grDevices stats annaffy: methods Biobase GO.db KEGG.db AnnotationDbi DBI CARNIVAL: doParallel readr viper AnnotationDbi Category ggplot2 UniProt.ws lpSolve igraph gdtools: Rcpp systemfonts SCATEData: ExperimentHub GenomicAlignments GenomicRanges base utils RforProteomics: MSnbase R.utils shiny biocViews BiocManager qPLEXanalyzer: Biobase MSnbase assertthat BiocGenerics Biostrings dplyr ggdendro ggplot2 graphics grDevices IRanges limma magrittr preprocessCore purrr RColorBrewer readr rlang scales stats stringr tibble tidyr tidyselect utils RcmdrMisc: utils car sandwich abind colorspace Hmisc MASS e1071 foreign haven readstata13 readxl graphics grDevices stats nortest lattice squash: graphics grDevices methods stats PREDA: Biobase lokern multtest stats methods annotate BSgenome.Celegans.UCSC.ce2: BSgenome BioMM: stats utils grDevices lattice BiocParallel glmnet rms precrec nsprcomp ranger e1071 ggplot2 vioplot CMplot imager topGO xlsx AnnotationFilter: utils methods GenomicRanges lazyeval biobroom: broom dplyr tidyr Biobase CCl4: Biobase limma svDialogs: svGUI utils methods rstudioapi coexnet: affy siggenes GEOquery vsn igraph acde Biobase limma graphics stats utils STRINGdb SummarizedExperiment minet rmarkdown dks: cubature readstata13: Rcpp BSgenome.Btaurus.UCSC.bosTau6.masked: BSgenome BSgenome.Btaurus.UCSC.bosTau6 ChromHeatMap: BiocGenerics annotate AnnotationDbi Biobase graphics grDevices methods stats IRanges rtracklayer GenomicRanges partykit: graphics grid libcoin mvtnorm grDevices stats utils survival Formula inum rpart MASS: grDevices graphics stats utils methods MAST: SingleCellExperiment Biobase BiocGenerics S4Vectors data.table ggplot2 plyr stringr abind methods parallel reshape2 stats stats4 graphics utils SummarizedExperiment progress MeasurementError.cor: org.Gg.eg.db: methods AnnotationDbi Biobase: BiocGenerics utils methods STAN: methods poilog parallel GenomicRanges IRanges S4Vectors BiocGenerics GenomeInfoDb Gviz Rsolnp dqrng: Rcpp BH sitmo survey: grid methods Matrix survival stats graphics splines lattice minqa numDeriv mitools IMMAN: STRINGdb Biostrings igraph graphics utils seqinr dichromat: stats flashClust: STATegRa: Biobase gridExtra ggplot2 methods stats grid MASS calibrate gplots edgeR limma foreach affy DEsingle: stats Matrix MASS VGAM bbmle gamlss maxLik pscl BiocParallel leeBamViews: Biobase Rsamtools BSgenome GenomicRanges GenomicAlignments methods S4Vectors parallel IRanges eisaR: graphics stats GenomicRanges GenomicFeatures S4Vectors IRanges AnnotationDbi limma edgeR methods SummarizedExperiment BiocGenerics rtracklayer utils sf: methods classInt DBI graphics grDevices grid magrittr Rcpp stats tools units utils fishpond: graphics stats utils methods abind gtools qvalue S4Vectors SummarizedExperiment matrixStats svMisc Rcpp Matrix combinat: dockerfiler: attempt glue R6 utils RefFreeEWAS: quadprog mitch: stats grDevices graphics utils MASS plyr reshape2 parallel GGally grid gridExtra knitr rmarkdown ggplot2 gplots beeswarm echarts4r seqCNA.annot: SPARQL: XML RCurl webshot: magrittr jsonlite callr sm: musicatk: NMF SummarizedExperiment VariantAnnotation cowplot Biostrings base methods magrittr tibble tidyr gtools gridExtra maftools MCMCprecision data.table dplyr rlang BSgenome GenomeInfoDb GenomicFeatures GenomicRanges IRanges S4Vectors uwot ggplot2 stringr TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene BSgenome.Hsapiens.UCSC.hg19 BSgenome.Hsapiens.UCSC.hg38 BSgenome.Mmusculus.UCSC.mm9 BSgenome.Mmusculus.UCSC.mm10 deconstructSigs decompTumor2Sig topicmodels ggrepel withr plotly utils sn: methods stats4 mnormt numDeriv utils quantreg base: dml: MASS lfda sp: methods utils stats graphics grDevices lattice grid rpx: methods BiocFileCache rappdirs xml2 RCurl utils logitT: affy cvTools: lattice robustbase stats ellipsis: rlang ASAFE: st: sda fdrtool corpcor graphics stats LRBaseDbi: methods stats utils AnnotationDbi RSQLite DBI Biobase berryFunctions: grDevices graphics stats utils abind dmt: methods mvtnorm MASS Matrix tiledb: methods Rcpp nanotime hgu95av2: qvcalc: GISPA: Biobase changepoint data.table genefilter graphics GSEABase HH lattice latticeExtra plyr scatterplot3d stats chromVAR: IRanges GenomeInfoDb GenomicRanges ggplot2 nabor BiocParallel BiocGenerics Biostrings TFBSTools Rsamtools S4Vectors methods Rcpp grid plotly shiny miniUI stats utils graphics DT Rtsne Matrix SummarizedExperiment RColorBrewer BSgenome RcppArmadillo clustvarsel: mclust stats Matrix BMA foreach iterators rqt: SummarizedExperiment stats Matrix ropls methods car RUnit metap CompQuadForm glmnet utils pls tm: NLP Rcpp parallel slam stats tools utils graphics xml2 BH scHOT: S4Vectors SingleCellExperiment Matrix SummarizedExperiment IRanges methods stats BiocParallel reshape ggplot2 igraph grDevices ggforce graphics TxRegInfra: RaggedExperiment mongolite methods rjson GenomicRanges IRanges BiocParallel GenomeInfoDb S4Vectors SummarizedExperiment utils FELLA: methods igraph Matrix KEGGREST plyr stats graphics utils CellScore: Biobase graphics grDevices gplots lsa methods RColorBrewer squash stats utils BioQC: Biobase edgeR Rcpp methods stats utils NOISeq: methods Biobase splines Matrix XML: methods utils deepSNV: methods graphics parallel IRanges GenomicRanges SummarizedExperiment Biostrings VGAM VariantAnnotation Rhtslib sigaR: Biobase CGHbase methods mvtnorm corpcor graphics igraph limma marray MASS penalized quadprog snowfall stats MethylAid: Biobase BiocParallel BiocGenerics ggplot2 grid gridBase grDevices graphics hexbin matrixStats minfi methods RColorBrewer shiny stats SummarizedExperiment utils ncGTW: methods BiocParallel xcms Rcpp grDevices graphics stats plogr: compiler: graphite: methods AnnotationDbi checkmate graph httr rappdirs stats utils rbibutils: utils tools rsm: estimability hgu133plus2.db: methods AnnotationDbi org.Hs.eg.db DIAlignR: methods stats zoo dplyr tidyr rlang mzR signal ggplot2 scales gridExtra RSQLite DBI Rcpp polylabelr: Rcpp ade4: graphics grDevices methods stats utils MASS pixmap sp progress scp: QFeatures methods stats utils SingleCellExperiment SummarizedExperiment MultiAssayExperiment S4Vectors dplyr magrittr rlang tRNA: GenomicRanges Structstrings stringr S4Vectors methods BiocGenerics IRanges XVector Biostrings Modstrings ggplot2 scales lme4: Matrix methods stats graphics grid splines utils parallel MASS lattice boot nlme minqa nloptr statmod Rcpp RcppEigen sda: entropy corpcor fdrtool graphics stats utils imageHTS: EBImage cellHTS2 tools Biobase hwriter methods vsn stats utils e1071 KEGGlincs: KOdata hgu133a.db org.Hs.eg.db AnnotationDbi KEGGgraph igraph plyr gtools httr RJSONIO KEGGREST methods graphics stats utils XML grDevices Heatplus: graphics grDevices stats RColorBrewer NBPSeq: splines qvalue scTGIF: GSEABase Biobase SingleCellExperiment BiocStyle plotly tagcloud rmarkdown Rcpp grDevices graphics utils knitr S4Vectors SummarizedExperiment RColorBrewer nnTensor methods scales msigdbr schex tibble ggplot2 igraph maxLik: miscTools methods sandwich tractor.base: methods ore reportr shades RNifti snow: utils CSSP: methods splines stats utils genoCN: graphics stats utils CSSQ: SummarizedExperiment GenomicRanges IRanges S4Vectors rtracklayer GenomicAlignments GenomicFeatures Rsamtools ggplot2 grDevices stats utils logNormReg: mosaicCore: stats dplyr rlang tidyr MASS getPass: utils rstudioapi FDb.InfiniumMethylation.hg18: GenomicFeatures TxDb.Hsapiens.UCSC.hg18.knownGene org.Hs.eg.db AnnotationDbi Biostrings FDb.InfiniumMethylation.hg19: GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene org.Hs.eg.db AnnotationDbi Biostrings diffGeneAnalysis: graphics grDevices minpack.lm stats utils distillery: unifiedWMWqPCR: methods BiocGenerics stats graphics HTqPCR Trendy: stats utils graphics grDevices segmented gplots parallel magrittr BiocParallel DT S4Vectors SummarizedExperiment methods shiny shinyFiles kebabs: Biostrings kernlab methods stats Rcpp Matrix XVector S4Vectors e1071 LiblineaR graphics grDevices utils apcluster IRanges flowUtils: Biobase graph methods stats utils corpcor RUnit XML flowCore miRLAB: methods stats utils RCurl httr stringr Hmisc energy entropy Roleswitch gplots glmnet impute limma pcalg TCGAbiolinks dplyr SummarizedExperiment ctc heatmap.plus InvariantCausalPrediction Category GOstats org.Hs.eg.db tweeDEseq: MASS limma edgeR parallel cqn R453Plus1Toolbox: methods VariantAnnotation Biostrings Biobase utils grDevices graphics stats tools xtable R2HTML TeachingDemos BiocGenerics S4Vectors IRanges XVector GenomicRanges SummarizedExperiment biomaRt BSgenome Rsamtools ShortRead org.Cf.eg.db: methods AnnotationDbi entropy: bigmemoryExtras: bigmemory methods drc: MASS stats car gtools multcomp plotrix scales uncoverappLib: markdown shiny shinyjs shinyBS shinyWidgets shinycssloaders DT Gviz Homo.sapiens openxlsx condformat stringr org.Hs.eg.db TxDb.Hsapiens.UCSC.hg38.knownGene BiocFileCache rappdirs TxDb.Hsapiens.UCSC.hg19.knownGene rlist utils EnsDb.Hsapiens.v75 EnsDb.Hsapiens.v86 OrganismDbi BSgenome.Hsapiens.UCSC.hg19 processx Rsamtools GenomicRanges rstudioapi: nnlasso: BaseSpaceR: RCurl RJSONIO methods org.Ag.eg.db: methods AnnotationDbi PROMISE: Biobase GSEABase stats RWeka: RWekajars rJava graphics stats utils grid alluvial: DEGraph: R.utils graph KEGGgraph lattice mvtnorm R.methodsS3 RBGL Rgraphviz rrcov NCIgraph earth: Formula plotmo TeachingDemos ruv: stats ggplot2 scales gridExtra cachem: rlang fastmap spotSegmentation: mclust Formula: stats doBy: methods broom curry Deriv dplyr ggplot2 MASS Matrix magrittr microbenchmark pbkrtest tibble here: rprojroot ArgumentCheck: RSVGTipsDevice: hgu133plus2CellScore: Biobase celaref: SummarizedExperiment MAST ggplot2 Matrix dplyr magrittr stats utils rlang BiocGenerics S4Vectors readr tibble DelayedArray futile.options: MSnbase: methods BiocGenerics Biobase mzR S4Vectors ProtGenerics BiocParallel IRanges plyr preprocessCore vsn grid stats4 affy impute pcaMethods MALDIquant mzID digest lattice ggplot2 XML scales MASS Rcpp basicTrendline: graphics stats scales investr SpidermiR: httr igraph utils stats miRNAtap miRNAtap.db AnnotationDbi org.Hs.eg.db ggplot2 gridExtra gplots grDevices lattice latticeExtra visNetwork TCGAbiolinks gdata MAGeCKFlute networkD3 psygenet2r: stringr RCurl igraph ggplot2 reshape2 grid parallel biomaRt BgeeDB topGO Biobase labeling GO.db later: Rcpp rlang Rbowtie: podkat: methods Rsamtools GenomicRanges Rcpp parallel stats graphics grDevices utils Biobase BiocGenerics Matrix GenomeInfoDb IRanges Biostrings BSgenome Rhtslib HiCDataLymphoblast: AnnotationForge: methods utils BiocGenerics Biobase AnnotationDbi DBI RSQLite XML S4Vectors RCurl ecp: Rcpp ReactomeGSA.data: limma edgeR ReactomeGSA Seurat rentrez: XML httr jsonlite colorRamps: CopyNumberPlots: karyoploteR regioneR IRanges Rsamtools SummarizedExperiment VariantAnnotation methods stats GenomeInfoDb GenomicRanges cn.mops rhdf5 utils PROPER: edgeR cleanUpdTSeq: BiocGenerics methods stats BSgenome GenomicRanges seqinr e1071 GenomeInfoDb IRanges utils BSgenome.Drerio.UCSC.danRer7 TCGAbiolinksGUI: shinydashboard TCGAbiolinksGUI.data shiny downloader grid DT plotly readr maftools stringr SummarizedExperiment ggrepel data.table caret shinyFiles ggplot2 pathview ELMER clusterProfiler parallel TCGAbiolinks shinyjs colourpicker sesame shinyBS zCompositions: methods MASS NADA truncnorm maptree: cluster rpart derfinderPlot: derfinder GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 graphics grDevices IRanges limma methods plyr RColorBrewer reshape2 S4Vectors scales utils gower: org.Hs.eg.db: methods AnnotationDbi readxl: cellranger Rcpp tibble utils progress canceR: tcltk tcltk2 cgdsr GSEABase tkrplot geNetClassifier RUnit Formula rpart survival Biobase phenoTest circlize plyr graphics stats utils grDevices genomewidesnp6Crlmm: utils prebs: GenomicAlignments affy RPA parallel methods stats GenomicRanges IRanges Biobase GenomeInfoDb S4Vectors NBSplice: methods edgeR stats MASS car mppa BiocParallel ggplot2 reshape2 DNABarcodes: Matrix parallel Rcpp BH rlang: utils SwathXtend: e1071 openxlsx VennDiagram lattice GGally: ggplot2 dplyr forcats grDevices grid gtable lifecycle plyr progress RColorBrewer reshape rlang scales tidyr utils magicaxis: grDevices graphics stats celestial MASS plotrix sm mapproj RColorBrewer RANN glmpca: MASS methods stats utils hgu133afrmavecs: funtooNorm: pls matrixStats minfi methods IlluminaHumanMethylation450kmanifest IlluminaHumanMethylation450kanno.ilmn12.hg19 GenomeInfoDb grDevices graphics stats dtw: proxy graphics grDevices stats utils xmlparsedata: RmiR.Hs.miRNA: AnnotationDbi lattice: grid grDevices graphics stats utils tweenr: Rcpp grDevices farver magrittr rlang EGSEAdata: hapmapsnp5: hapmapsnp6: DNAshapeR: GenomicRanges Rcpp Biostrings fields MAQCsubset: affy Biobase lumi methods gcapc: BiocGenerics GenomeInfoDb S4Vectors IRanges Biostrings BSgenome GenomicRanges Rsamtools GenomicAlignments matrixStats MASS splines grDevices graphics stats methods mapscape: htmlwidgets jsonlite base64enc stringr rcmdcheck: callr cli crayon desc digest pkgbuild prettyunits R6 rprojroot sessioninfo utils withr xopen biotmle: stats methods dplyr tibble ggplot2 ggsci superheat assertthat future doFuture drtmle S4Vectors BiocGenerics BiocParallel SummarizedExperiment limma cobs: SparseM quantreg grDevices graphics splines stats methods trena: utils glmnet MotifDb RSQLite RMySQL lassopv randomForest vbsr xgboost BiocParallel RPostgreSQL methods DBI BSgenome BSgenome.Hsapiens.UCSC.hg38 BSgenome.Hsapiens.UCSC.hg19 BSgenome.Mmusculus.UCSC.mm10 SNPlocs.Hsapiens.dbSNP150.GRCh38 org.Hs.eg.db Biostrings GenomicRanges biomaRt AnnotationDbi grasp2db: RSQLite dplyr dbplyr methods utils stats GenomeInfoDb AnnotationHub digest banocc: rstan coda mvtnorm stringr depmixS4: nnet MASS Rsolnp nlme stats stats4 methods adductData: ExperimentHub AnnotationHub stats utils methods datasets destiny: methods graphics grDevices utils stats Matrix Rcpp RcppEigen RSpectra irlba pcaMethods Biobase BiocGenerics SummarizedExperiment SingleCellExperiment ggplot2 ggplot.multistats tidyr tidyselect ggthemes VIM knn.covertree proxy RcppHNSW smoother scales scatterplot3d AIMS: e1071 Biobase plsVarSel: pls grDevices graphics genalg mvtnorm bdsmatrix MASS progress parallel stats MSQC praznik profileModel: heatmaps: methods grDevices graphics stats Biostrings GenomicRanges IRanges KernSmooth plotrix Matrix EBImage RColorBrewer BiocGenerics GenomeInfoDb BiocVersion: scDD: fields mclust BiocParallel outliers ggplot2 EBSeq arm SingleCellExperiment SummarizedExperiment grDevices graphics stats S4Vectors scran VegaMC: biomaRt Biobase methods genoset ssrch: methods shiny DT utils ALLMLL: affy annotationTools: Biobase stats SuperLearner: nnls cvAUC recoup: GenomicRanges GenomicAlignments ggplot2 ComplexHeatmap BiocGenerics biomaRt circlize GenomeInfoDb GenomicFeatures graphics grDevices httr methods parallel RSQLite Rsamtools rtracklayer S4Vectors stats stringr utils fastseg: GenomicRanges Biobase methods graphics stats BiocGenerics S4Vectors IRanges BiocStyle: bookdown knitr rmarkdown stats utils yaml BiocManager coda: lattice cisPath: methods utils GENIE3: stats reshape2 QUBICdata: stjudem: utils isa2: methods grDevices lattice stats utils IntramiRExploreR: igraph FGNet knitr stats utils grDevices graphics xgboost: Matrix methods data.table magrittr jsonlite EMDomics: emdist BiocParallel matrixStats ggplot2 CDFt preprocessCore scran: SingleCellExperiment SummarizedExperiment S4Vectors BiocGenerics BiocParallel Rcpp stats methods utils Matrix scuttle edgeR limma BiocNeighbors igraph statmod DelayedArray DelayedMatrixStats BiocSingular bluster dqrng beachmat BH egg: gridExtra ggplot2 gtable grid grDevices utils DEScan2: GenomicRanges BiocParallel BiocGenerics ChIPpeakAnno data.table DelayedArray GenomeInfoDb GenomicAlignments glue IRanges plyr Rcpp rtracklayer S4Vectors SummarizedExperiment tools utils RcppArmadillo BiocSet: dplyr methods tibble utils rlang plyr S4Vectors BiocIO AnnotationDbi KEGGREST ontologyIndex tidyr QSutils: Biostrings BiocGenerics methods ape stats psych qgraph: Rcpp methods grDevices psych lavaan plyr Hmisc igraph jpeg png colorspace Matrix corpcor reshape2 ggplot2 glasso fdrtool gtools parallel pbapply abind dplyr gWidgets2RGtk2: methods memoise RGtk2 gWidgets2 svglite: systemfonts cpp11 ProteomicsAnnotationHubData: AnnotationHub AnnotationHubData mzR MSnbase Biostrings GenomeInfoDb utils Biobase BiocManager RCurl PrInCE: purrr dplyr tidyr forecast progress Hmisc naivebayes robustbase ranger LiblineaR speedglm tester magrittr Biobase MSnbase stats utils methods Rdpack rapportools: reshape plyr pander PanVizGenerator: methods shiny tools jsonlite pcaMethods FindMyFriends igraph stats utils MultiMed: pushbar: shiny jsonlite BSgenome.Mmusculus.UCSC.mm10: BSgenome eiR: ChemmineR methods DBI snow tools snowfall RUnit RCurl digest BiocGenerics gespeR RcppAnnoy celda: plyr foreach ggplot2 RColorBrewer grid scales gtable grDevices graphics matrixStats doParallel digest methods reshape2 MAST S4Vectors data.table Rcpp RcppEigen uwot enrichR stringi SummarizedExperiment MCMCprecision ggrepel Rtsne withr dendextend ggdendro pROC scater scran SingleCellExperiment dbscan DelayedArray Seurat stringr Matrix ComplexHeatmap multipanelfigure circlize beachmat: methods DelayedArray BiocGenerics Matrix stats: utils grDevices graphics IdeoViz: Biobase IRanges GenomicRanges RColorBrewer rtracklayer graphics GenomeInfoDb RGalaxy: XML methods tools optparse BiocGenerics Biobase roxygen2 naturalsort: NADA: methods survival poibin: enrichR: httr rjson ggplot2 onlineFDR: stats Xeva: methods stats utils BBmisc Biobase grDevices ggplot2 scales ComplexHeatmap parallel doParallel Rmisc grid nlme PharmacoGx downloader cMap2data: methylPipe: methods grDevices graphics stats utils GenomicRanges SummarizedExperiment Rsamtools marray gplots IRanges BiocGenerics Gviz GenomicAlignments Biostrings parallel data.table GenomeInfoDb S4Vectors scTensor: methods RSQLite igraph S4Vectors plotly reactome.db AnnotationDbi SummarizedExperiment SingleCellExperiment nnTensor rTensor abind plotrix heatmaply tagcloud rmarkdown BiocStyle knitr AnnotationHub MeSHDbi grDevices graphics stats utils outliers Category meshr GOstats ReactomePA DOSE crayon checkmate BiocManager visNetwork schex ggplot2 SAVER: glmnet foreach methods iterators doParallel Matrix qrqc: reshape ggplot2 Biostrings biovizBase brew xtable testthat graphics methods plyr stats Rhtslib tmle: glmnet SuperLearner circRNAprofiler: dplyr magrittr readr rtracklayer stringr stringi DESeq2 edgeR GenomicRanges IRanges seqinr R.utils reshape2 ggplot2 utils rlang S4Vectors stats GenomeInfoDb universalmotif AnnotationHub BSgenome.Hsapiens.UCSC.hg19 Biostrings gwascat BSgenome NCIgraph: graph KEGGgraph methods RBGL RCy3 R.methodsS3 MSnID: Rcpp MSnbase mzID R.cache foreach doParallel parallel methods iterators data.table Biobase ProtGenerics reshape2 dplyr mzR BiocStyle msmsTests ggplot2 RUnit BiocGenerics Biostrings purrr rlang stringr tibble AnnotationHub AnnotationDbi xtable KernSmooth: stats rGREAT: GenomicRanges IRanges methods rjson GetoptLong RCurl utils stats TENxBUSData: ExperimentHub AnnotationHub utils BiocGenerics imp4p: Iso stats truncnorm norm missForest missMDA Rcpp pbivnorm: GRmetrics: SummarizedExperiment drc plotly ggplot2 S4Vectors stats randomcoloR: colorspace stringr V8 stats methods scales Rtsne grDevices cluster derfinderHelper: IRanges Matrix methods S4Vectors NetRep: methods foreach Rcpp statmod RhpcBLASctl abind RColorBrewer utils stats graphics grDevices BH RcppArmadillo MBQN: stats graphics utils limma SummarizedExperiment preprocessCore BiocFileCache rappdirs rpx xml2 RCurl ggplot2 PairedData evaluomeR: SummarizedExperiment MultiAssayExperiment cluster fpc randomForest flexmix corrplot grDevices graphics reshape2 ggplot2 ggdendro plotrix stats matrixStats Rdpack MASS class prabclus mclust kableExtra profileplyr: BiocGenerics SummarizedExperiment GenomicRanges stats soGGi methods utils S4Vectors R.utils dplyr magrittr tidyr IRanges rjson ChIPseeker 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 Cairo tiff snapCGH: aCGH cluster DNAcopy GLAD graphics grDevices limma methods stats tilingArray utils optimalFlowData: IONiseR: rhdf5 dplyr magrittr tidyr ShortRead Biostrings ggplot2 methods BiocGenerics XVector tibble stats BiocParallel bit64 stringr utils escape: grDevices dplyr ggplot2 GSEABase GSVA SingleCellExperiment limma ggridges msigdbr stats BiocParallel Matrix rjson: tofsimsData: sna: utils statnet.common network RIVER: glmnet pROC ggplot2 graphics stats Biobase methods utils heatmap3: fastcluster parmigene: doMC: foreach iterators parallel utils MatrixCorrelation: Rcpp plotrix pracma progress RSpectra RcppArmadillo paircompviz: Rgraphviz safe: AnnotationDbi Biobase methods SparseM signatureSearch: Rcpp SummarizedExperiment 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 iasva: irlba stats cluster graphics SummarizedExperiment BiocParallel SmartSVA: sva isva RSpectra Rcpp stats utils RcppEigen cytofast: flowCore ggplot2 ggridges RColorBrewer reshape2 stats grDevices Rdpack methods grid FlowSOM brgedata: Biobase SummarizedExperiment RcppNumerical: Rcpp RcppEigen NetPreProc: methods graph recount3: SummarizedExperiment BiocFileCache methods rtracklayer S4Vectors utils RCurl data.table R.utils Matrix GenomicRanges sessioninfo tools snm: corpcor lme4 splines PeacoQC: circlize ComplexHeatmap flowCore flowWorkspace ggplot2 grDevices grid gridExtra methods plyr stats utils FactoMineR: car cluster DT ellipse flashClust graphics grDevices lattice leaps MASS scatterplot3d stats utils ggplot2 ggrepel Guitar: GenomicFeatures rtracklayer AnnotationDbi GenomicRanges magrittr ggplot2 methods stats utils knitr dplyr bcSeq: Rcpp Matrix Biostrings Structstrings: S4Vectors IRanges Biostrings methods BiocGenerics XVector stringr stringi crayon grDevices UpSetR: ggplot2 gridExtra plyr utils stats methods grDevices scales Informeasure: entropy matrixStats XBSeq: DESeq2 pracma matrixStats locfit ggplot2 methods Biobase dplyr magrittr roar idr2d: dplyr futile.logger GenomeInfoDb GenomicRanges ggplot2 grDevices idr IRanges magrittr methods reticulate scales stats stringr utils dcanr: igraph foreach plyr stringr reshape2 methods Matrix graphics stats RColorBrewer circlize doRNG DMCHMM: SummarizedExperiment methods S4Vectors BiocParallel GenomicRanges IRanges fdrtool utils stats grDevices rtracklayer multcomp calibrate graphics sizepower: stats OutlierD: Biobase quantreg datamods: htmltools shiny shinyWidgets DT data.table readxl rio rlang tibble tools assertive.data.uk: assertive.base assertive.strings import: cfDNAPro: magrittr stats utils dplyr stringr quantmod ggplot2 Rsamtools rlang som: fastmatch: VCFArray: methods BiocGenerics DelayedArray tools GenomicRanges VariantAnnotation GenomicFiles S4Vectors Rsamtools treeio: ape dplyr jsonlite magrittr methods rlang tibble tidytree utils methylGSA: RobustRankAggreg ggplot2 stringr stats clusterProfiler missMethyl org.Hs.eg.db reactome.db BiocParallel GO.db AnnotationDbi shiny IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylationEPICanno.ilm10b4.hg19 BSgenome.Drerio.UCSC.danRer10: BSgenome cvAUC: ROCR data.table RnBeads.mm9: GenomicRanges assertive.data.us: assertive.base assertive.strings shinyTree: methods shiny htmlwidgets jsonlite stringr promises rcdk: rcdklibs fingerprint rJava methods png iterators itertools Rmagpie: Biobase e1071 graphics grDevices kernlab methods pamr stats utils HMMcopy: data.table flowMerge: graph feature flowClust Rgraphviz foreach snow rrcov flowCore graphics methods stats utils coin: survival methods parallel stats stats4 utils libcoin matrixStats modeltools mvtnorm multcomp M3Drop: numDeriv RColorBrewer gplots bbmle statmod grDevices graphics stats matrixStats Matrix irlba reldist Hmisc methods hummingbird: Rcpp graphics GenomicRanges SummarizedExperiment IRanges qsea: Biostrings graphics gtools methods stats utils HMMcopy rtracklayer BSgenome GenomicRanges Rsamtools IRanges limma GenomeInfoDb BiocGenerics grDevices zoo BiocParallel KernSmooth MASS flowWorkspace: Biobase BiocGenerics cytolib lattice latticeExtra XML ggplot2 graph graphics grDevices methods stats stats4 utils RBGL tools Rgraphviz data.table dplyr Rcpp scales matrixStats RcppParallel RProtoBufLib digest aws.s3 aws.signature flowCore ncdfFlow BH Rhdf5lib RcppArmadillo yaImpute: grDevices graphics stats utils RNeXML: ape methods XML plyr reshape2 httr uuid dplyr lazyeval tidyr stringr stringi xml2 truncnorm: princurve: stats graphics grDevices Rcpp GSALightning: Matrix data.table stats spp: Rcpp Rsamtools caTools parallel graphics stats BH macrophage: gistr: jsonlite crul httr magrittr assertthat knitr rmarkdown dplyr igraphdata: REDseq: BiocGenerics BSgenome.Celegans.UCSC.ce2 multtest Biostrings BSgenome ChIPpeakAnno AnnotationDbi graphics IRanges stats utils lmom: stats graphics RTCGA.clinical: RTCGA idpr: ggplot2 magrittr dplyr plyr jsonlite rlang Biostrings methods spatstat.core: spatstat.data spatstat.geom stats graphics grDevices utils methods nlme rpart spatstat.utils spatstat.sparse mgcv Matrix abind tensor goftest fontLiberation: sSeq: caTools RColorBrewer daMA: MASS stats GeneNetworkBuilder: Rcpp plyr graph htmlwidgets Rgraphviz rjson XML methods grDevices stats graphics RTCGA.miRNASeq: RTCGA RGtk2: methods Rmisc: lattice plyr atSNP: BSgenome BiocFileCache BiocParallel Rcpp data.table ggplot2 grDevices graphics grid motifStack rappdirs stats testthat utils lifecycle pbkrtest: lme4 broom dplyr magrittr MASS Matrix methods numDeriv parallel knitr Polychrome: colorspace scatterplot3d methods graphics grDevices stats utils TFisher: stats sn mvtnorm Matrix gscreend: SummarizedExperiment nloptr fGarch methods BiocParallel graphics cola: grDevices graphics grid stats utils ComplexHeatmap matrixStats GetoptLong circlize GlobalOptions clue parallel RColorBrewer cluster skmeans png mclust crayon methods xml2 microbenchmark httr knitr markdown digest impute brew Rcpp BiocGenerics eulerr colortools: TCGAutils: AnnotationDbi BiocGenerics GenomeInfoDb GenomicFeatures GenomicRanges GenomicDataCommons IRanges methods MultiAssayExperiment RaggedExperiment rvest S4Vectors stats stringr SummarizedExperiment utils xml2 GenomicTuples: GenomicRanges GenomeInfoDb S4Vectors methods BiocGenerics Rcpp IRanges data.table stats4 stats utils curatedMetagenomicData: AnnotationHub Biobase dplyr ExperimentHub magrittr methods S4Vectors tidyr utils labelled: haven dplyr lifecycle rlang vctrs stringr tidyr tigre: BiocGenerics Biobase methods AnnotationDbi gplots graphics grDevices stats utils annotate DBI RSQLite pastecs: boot stats graphics utils grDevices rematch2: tibble linkcomm: igraph RColorBrewer dynamicTreeCut grid utils monocle: methods Matrix Biobase ggplot2 VGAM DDRTree parallel igraph BiocGenerics HSMMSingleCell plyr cluster combinat fastICA grid irlba matrixStats densityClust Rtsne MASS reshape2 limma tibble dplyr qlcMatrix pheatmap stringr proxy slam viridis stats biocViews RANN Rcpp BiFET: stats poibin GenomicRanges org.Ss.eg.db: methods AnnotationDbi hgu133a.db: methods AnnotationDbi org.Hs.eg.db LaplacesDemon: parallel grDevices graphics stats utils bezier: GSEABase: BiocGenerics Biobase annotate methods graph AnnotationDbi XML 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 RadioGx: CoreGx SummarizedExperiment S4Vectors Biobase parallel BiocParallel RColorBrewer caTools magicaxis methods reshape2 scales grDevices graphics stats utils assertthat matrixStats downloader RMassBank: Rcpp XML rjson S4Vectors digest rcdk yaml mzR methods Biobase MSnbase httr enviPat assertthat colr: hgu95av2probe: AnnotationDbi iCOBRA: shiny shinydashboard shinyBS reshape2 ggplot2 scales ROCR dplyr DT limma methods UpSetR rebus.datetimes: rebus.base PWMEnrich: methods grid BiocGenerics Biostrings seqLogo gdata evd S4Vectors CopyhelpeR: shinyMethyl: methods BiocGenerics shiny minfi IlluminaHumanMethylation450kmanifest matrixStats RColorBrewer ASpediaFI: SummarizedExperiment ROCR BiocParallel GenomicAlignments GenomicFeatures GenomicRanges IRanges IVAS Rsamtools biomaRt limma S4Vectors stats DRaWR GenomeInfoDb Gviz Matrix dplyr fgsea reshape2 igraph graphics e1071 methods rtracklayer scales grid ggplot2 mGSZ utils IlluminaHumanMethylationEPICanno.ilm10b2.hg19: minfi DEComplexDisease: Rcpp DESeq2 edgeR SummarizedExperiment ComplexHeatmap grid parallel BiocParallel grDevices graphics stats methods utils GenomicState: AnnotationHub GenomicFeatures GenomeInfoDb rtracklayer bumphunter derfinder AnnotationDbi IRanges org.Hs.eg.db utils methods Streamer: methods graph RBGL parallel BiocGenerics BDMMAcorrect: vegan ellipse ggplot2 ape SummarizedExperiment Rcpp RcppArmadillo RcppEigen stats mirIntegrator: graph ROntoTools ggplot2 org.Hs.eg.db AnnotationDbi Rgraphviz blastula: base64enc commonmark curl digest dplyr fs getPass here htmltools httr jsonlite magrittr mime rlang rmarkdown stringr uuid scPipe: ggplot2 methods SingleCellExperiment Rhtslib biomaRt GGally MASS mclust Rcpp reshape BiocGenerics robustbase scales utils stats S4Vectors SummarizedExperiment AnnotationDbi org.Hs.eg.db org.Mm.eg.db stringr rtracklayer hash dplyr GenomicRanges magrittr glue rlang scater zlibbioc testthat ggrastr: ggplot2 Cairo ggbeeswarm grid png ragg optimx: numDeriv BitSeq: Rsamtools S4Vectors IRanges Rhtslib epivizrChart: epivizrData epivizrServer htmltools rjson methods BiocGenerics aws.s3: utils tools curl httr xml2 base64enc digest aws.signature GMRP: stats utils graphics grDevices diagram plotrix base GenomicRanges RnaSeqSampleSizeData: edgeR HybridMTest: Biobase fdrtool MASS survival stats tradeSeq: mgcv edgeR SingleCellExperiment SummarizedExperiment slingshot magrittr RColorBrewer BiocParallel Biobase pbapply ggplot2 princurve methods monocle igraph S4Vectors tibble Matrix viridis matrixStats startupmsg: inaparc: kpeaks lhs stats methods gMWT: clinfun Rcpp RcppArmadillo CopywriteR: BiocParallel matrixStats gtools data.table S4Vectors chipseq IRanges Rsamtools DNAcopy GenomicAlignments GenomicRanges CopyhelpeR GenomeInfoDb futile.logger icetea: stats utils methods graphics grDevices ggplot2 GenomicFeatures ShortRead BiocParallel Biostrings S4Vectors Rsamtools BiocGenerics IRanges GenomicAlignments GenomicRanges rtracklayer SummarizedExperiment VariantAnnotation limma edgeR csaw DESeq2 TxDb.Dmelanogaster.UCSC.dm6.ensGene epivizrServer: methods httpuv R6 rjson mime httr: curl jsonlite mime openssl R6 assertive.numbers: assertive.base radiant.data: magrittr ggplot2 lubridate tidyr dplyr tibble rlang broom car knitr markdown rmarkdown shiny jsonlite shinyAce psych DT readr readxl writexl scales curl rstudioapi import plotly glue shinyFiles stringi randomizr patchwork MASS base64enc CNVRanger: GenomicRanges RaggedExperiment BiocGenerics BiocParallel GDSArray GenomeInfoDb IRanges S4Vectors SNPRelate SummarizedExperiment data.table edgeR gdsfmt grDevices lattice limma methods plyr qqman rappdirs reshape2 stats utils DirichletReg: Formula stats graphics methods maxLik sva: mgcv genefilter BiocParallel matrixStats stats graphics utils limma edgeR samr: impute matrixStats shiny shinyFiles openxlsx GSA pgca: utils stats spam: dotCall64 grid methods qlcMatrix: Matrix slam sparsesvd methods docopt metaseqR2: DESeq2 limma locfit splines ABSSeq baySeq Biobase BiocGenerics BiocParallel biomaRt Biostrings corrplot DSS DT EDASeq edgeR genefilter GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gplots graphics grDevices harmonicmeanp heatmaply htmltools httr IRanges jsonlite lattice log4r magrittr MASS Matrix methods NBPSeq pander parallel qvalue rmarkdown rmdformats Rsamtools RSQLite rtracklayer S4Vectors stats stringr SummarizedExperiment survcomp utils VennDiagram vsn yaml zoo svd: methods interactiveDisplayBase: methods BiocGenerics shiny DT shiny: methods utils grDevices httpuv mime jsonlite xtable digest htmltools R6 sourcetools later promises tools crayon rlang fastmap withr commonmark glue bslib cachem ellipsis lifecycle RTCGA: XML assertthat stringi rvest data.table xml2 dplyr purrr survival survminer ggplot2 ggthemes viridis knitr scales ABAEnrichment: Rcpp gplots gtools ABAData data.table GOfuncR grDevices stats graphics utils CNORode: CellNOptR genalg markdown: utils xfun mime polynom: stats graphics coop: copa: Biobase methods INDEED: glasso devtools graphics stats utils igraph visNetwork AhoCorasickTrie: Rcpp randPack: methods Biobase breastCancerUPP: PepsNMRData: methylCC: FlowSorted.Blood.450k Biobase GenomicRanges IRanges S4Vectors dplyr magrittr minfi bsseq quadprog plyranges stats utils bumphunter genefilter methods IlluminaHumanMethylation450kmanifest IlluminaHumanMethylation450kanno.ilmn12.hg19 rexposome: Biobase methods utils stats lsr FactoMineR stringr circlize corrplot ggplot2 reshape2 pryr S4Vectors imputeLCMD scatterplot3d glmnet gridExtra grid Hmisc gplots gtools scales lme4 grDevices graphics ggrepel mice calm: mgcv stats graphics ashr: Matrix stats graphics Rcpp truncnorm mixsqp SQUAREM etrunct invgamma graphics: grDevices kableExtra: knitr magrittr stringr xml2 rvest rmarkdown scales viridisLite stats grDevices htmltools rstudioapi glue tools webshot digest graphics svglite org.Mm.eg.db: methods AnnotationDbi TH.data: survival MASS geepack: methods MASS broom magrittr dittoSeq: ggplot2 methods colorspace gridExtra cowplot reshape2 pheatmap grDevices ggrepel ggridges stats utils SummarizedExperiment SingleCellExperiment edgeR S4Vectors IntEREst: GenomicRanges Rsamtools SummarizedExperiment edgeR S4Vectors seqLogo Biostrings GenomicFeatures IRanges seqinr graphics grDevices stats utils grid methods DBI RMySQL GenomicAlignments BiocParallel BiocGenerics DEXSeq DESeq2 flowPloidy: flowCore car caTools knitr rmarkdown minpack.lm shiny methods graphics stats utils singscore: methods stats graphics ggplot2 grDevices ggrepel GSEABase plotly tidyr plyr magrittr reshape edgeR RColorBrewer Biobase BiocParallel SummarizedExperiment matrixStats reshape2 S4Vectors timsac: graphics grDevices stats fda: splines Matrix fds xfun: stats tools huge: Matrix igraph MASS grDevices graphics methods stats utils Rcpp RcppEigen shinythemes: shiny STROMA4: Biobase BiocParallel cluster matrixStats stats graphics utils distr: methods graphics startupmsg sfsmisc stats grDevices utils MASS mQTL: qtl MASS outliers ArrayExpress: Biobase XML oligo limma RTCGA.mRNA: RTCGA BiocManager: utils MPRAnalyze: BiocParallel methods progress stats SummarizedExperiment unmarked: methods lattice graphics stats utils parallel plyr raster Matrix MASS Rcpp RcppArmadillo profmem: utils ADaCGH2: parallel ff GLAD bit ffbase DNAcopy tilingArray waveslim cluster aCGH snapCGH rclipboard: shiny PRIMME: Rcpp Matrix fds: rainbow RCurl assertive.properties: assertive.base methods ASICSdata: gcspikelite: dcGSA: Matrix BiocParallel debrowser: shiny jsonlite shinyjs shinydashboard shinyBS gplots DT ggplot2 RColorBrewer annotate AnnotationDbi DESeq2 DOSE igraph grDevices graphics stats utils GenomicRanges IRanges S4Vectors SummarizedExperiment stringi reshape2 org.Hs.eg.db org.Mm.eg.db limma edgeR clusterProfiler methods sva RCurl enrichplot colourpicker plotly heatmaply Harman pathview apeglm ashr compcodeR: sm tcltk knitr markdown ROCR lattice gplots gtools gdata caTools grid KernSmooth MASS ggplot2 stringr modeest edgeR limma vioplot methods utils stats grDevices graphics STRINGdb: png sqldf plyr igraph RCurl methods RColorBrewer gplots hash plotrix dnet: igraph supraHex graph Rgraphviz Matrix RTNsurvival: RTN RTNduals methods survival RColorBrewer grDevices graphics stats utils scales data.table egg ggplot2 pheatmap dunn.test CNVtools: survival Nebulosa: ggplot2 patchwork Seurat SingleCellExperiment SummarizedExperiment SeuratObject ks Matrix stats methods EBSEA: DESeq2 graphics stats EmpiricalBrownsMethod EventPointer: SGSeq Matrix SummarizedExperiment GenomicFeatures stringr GenomeInfoDb igraph MASS nnls limma matrixStats RBGL prodlim graph methods utils stats doParallel foreach affxparser GenomicRanges S4Vectors IRanges qvalue cobs rhdf5 BSgenome BSgenome.Hsapiens.UCSC.hg38 Biostrings AffymetrixDataTestFiles: ggtree: ape aplot dplyr ggplot2 grid magrittr methods purrr rlang rvcheck tidyr tidytree treeio utils scales HIREewas: quadprog gplots grDevices stats globals: codetools Omixer: dplyr ggplot2 forcats tibble gridExtra magrittr readr tidyselect grid stats stringr pracma: graphics grDevices stats utils networkBMA: stats utils BMA Rcpp RcppArmadillo RcppEigen leaps BH plotly: ggplot2 tools scales httr jsonlite magrittr digest viridisLite base64enc htmltools htmlwidgets tidyr RColorBrewer dplyr vctrs tibble lazyeval rlang crosstalk purrr data.table promises RcppArmadillo: Rcpp stats utils methods evd: stats grDevices graphics hgu133a2.db: methods AnnotationDbi org.Hs.eg.db IRanges: methods utils stats BiocGenerics S4Vectors stats4 diffcoexp: WGCNA SummarizedExperiment stats DiffCorr psych igraph BiocGenerics sys: ggstar: grid utils ggplot2 scales gridExtra plotmo: Formula plotrix TeachingDemos GWASdata: GWASTools CGEN: survival mvtnorm reactable: digest htmltools htmlwidgets jsonlite reactR convert: Biobase limma marray utils methods MIGSA: methods BiocGenerics AnnotationDbi Biobase BiocParallel compiler data.table edgeR futile.logger ggdendro ggplot2 GO.db GOstats graph graphics grDevices grid GSEABase ismev jsonlite limma matrixStats org.Hs.eg.db RBGL reshape2 Rgraphviz stats utils vegan hom.Mm.inp.db: methods AnnotationDbi MantelCorr: stats HiCcompare: dplyr data.table ggplot2 gridExtra mgcv stats InteractionSet GenomicRanges IRanges S4Vectors BiocParallel QDNAseq KernSmooth methods utils graphics pheatmap gtools rhdf5 Rariant: GenomicRanges VariantAnnotation methods BiocGenerics S4Vectors IRanges GenomeInfoDb ggbio ggplot2 exomeCopy SomaticSignatures Rsamtools shiny VGAM dplyr reshape2 inline: methods checkmate: backports utils DMRforPairs: Gviz R2HTML GenomicRanges parallel zlibbioc: scruff: data.table GenomicAlignments GenomicFeatures GenomicRanges Rsamtools ShortRead parallel plyr BiocGenerics BiocParallel S4Vectors AnnotationDbi Biostrings methods ggplot2 ggthemes scales GenomeInfoDb stringdist ggbio rtracklayer SingleCellExperiment SummarizedExperiment Rsubread cn.farms: Biobase methods ff oligoClasses snow DBI affxparser oligo DNAcopy preprocessCore lattice philr: ape phangorn tidyr ggplot2 ggtree nanotime: methods bit64 RcppCCTZ zoo Rcpp RcppDate BioNet: graph RBGL igraph AnnotationDbi Biobase LiquidAssociation: geepack methods yeastCC org.Sc.sgd.db Biobase graphics grDevices stats ggthemes: ggplot2 graphics grid methods purrr scales stringr tibble parallelly: parallel tools utils GmicR: AnnotationDbi ape bnlearn Category DT doParallel foreach gRbase GSEABase gRain GOstats org.Hs.eg.db org.Mm.eg.db shiny WGCNA data.table grDevices graphics reshape2 stats utils modeest: fBasics stable stabledist stats statip LBE: stats graphics grDevices methods utils breastCancerVDX: grplasso: methods corpcor: stats magic: abind cbaf: BiocFileCache RColorBrewer cgdsr genefilter gplots grDevices stats utils xlsx ncdf4: compEpiTools: methods topGO GenomicRanges AnnotationDbi BiocGenerics Biostrings Rsamtools parallel grDevices gplots IRanges GenomicFeatures XVector methylPipe GO.db S4Vectors GenomeInfoDb SomaticCancerAlterations: GenomicRanges exomeCopy stringr IRanges S4Vectors sass: digest fs rlang htmltools R6 rappdirs proActiv: dplyr GenomicRanges GenomicFeatures GenomicAlignments GenomeInfoDb IRanges S4Vectors methods rlang SummarizedExperiment AnnotationDbi DESeq2 data.table tibble Gviz BiocParallel OVESEG: stats utils methods BiocParallel SummarizedExperiment limma fdrtool Rcpp M3C: ggplot2 Matrix doSNOW cluster parallel foreach doParallel matrixcalc Rtsne corpcor umap R.filesets: R.oo digest R.methodsS3 R.utils R.cache stats puma: oligo graphics grDevices methods stats utils mclust oligoClasses Biobase affy affyio genoset: BiocGenerics GenomicRanges SummarizedExperiment S4Vectors GenomeInfoDb IRanges methods graphics phylogram: ape methods stats config: yaml RJMCMCNucleosomes: IRanges GenomicRanges Rcpp consensusSeekeR BiocGenerics GenomeInfoDb S4Vectors BiocParallel stats graphics methods grDevices mouse4302.db: methods AnnotationDbi org.Mm.eg.db minfiDataEPIC: minfi IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICanno.ilm10b2.hg19 lipidr: SummarizedExperiment methods stats utils data.table S4Vectors rlang dplyr tidyr forcats ggplot2 limma fgsea ropls imputeLCMD magrittr flagme: gcspikelite xcms CAMERA gplots graphics MASS methods SparseM stats utils limSolve: quadprog lpSolve MASS ProtGenerics: methods GSBenchMark: readr: cli clipr crayon hms methods rlang R6 tibble utils lifecycle BH cpp11 savR: ggplot2 methods reshape2 scales gridExtra XML digest: utils shinypanel: shinyjs shiny shinyBS htmltools jsonlite RSEIS: RPMG Rwave corrplot: usethis: cli clipr crayon curl desc fs gert gh glue jsonlite lifecycle purrr rappdirs rlang rprojroot rstudioapi stats utils whisker withr yaml sesameData: ExperimentHub AnnotationHub rmarkdown utils curl globalSeq: MethylAidData: MethylAid PLPE: Biobase LPE MASS methods PasillaTranscriptExpr: LRBase.Mmu.eg.db: LRBaseDbi RSQLite caOmicsV: igraph bc3net covr: methods digest stats utils jsonlite rex httr crayon withr yaml diffr: htmlwidgets omicsPrint: MASS methods matrixStats graphics stats SummarizedExperiment MultiAssayExperiment RaggedExperiment massiR: cluster gplots diptest Biobase LEA: methods stats utils graphics cluster: graphics grDevices stats utils GUniFrac: matrixStats Matrix vegan ape parallel stats utils DepecheR: ggplot2 MASS Rcpp dplyr gplots viridis foreach doSNOW matrixStats mixOmics moments grDevices graphics stats utils methods parallel reshape2 beanplot FNN robustbase gmodels RcppEigen forecast: colorspace fracdiff ggplot2 graphics lmtest magrittr nnet parallel Rcpp stats timeDate tseries urca zoo RcppArmadillo spatstat.data: spatstat.utils Matrix msPurityData: googledrive: curl gargle glue httr jsonlite magrittr purrr rlang tibble utils uuid umap: methods openssl reticulate Rcpp RSpectra stats Iso: tidyselect: ellipsis glue purrr rlang vctrs RNAdecay: stats grDevices grid ggplot2 gplots utils TMB nloptr scales aroma.core: R.utils R.filesets R.devices stats tools utils R.methodsS3 R.oo R.cache R.rsp matrixStats RColorBrewer PSCBS listenv future BiocManager reticulate: Matrix Rcpp graphics jsonlite methods png rappdirs utils withr gamlss.data: chromstaR: GenomicRanges ggplot2 chromstaRData methods utils grDevices graphics stats foreach doParallel BiocGenerics S4Vectors GenomeInfoDb IRanges reshape2 Rsamtools GenomicAlignments bamsignals mvtnorm HumanAffyData: ExperimentHub Biobase e1071: graphics grDevices class stats methods utils proxy TEQC: methods BiocGenerics IRanges Rsamtools hwriter Biobase adehabitatMA: sp methods utils graphics grDevices stats filehash ddPCRclust: plotrix clue parallel ggplot2 openxlsx R.utils flowCore flowDensity SamSPECTRAL flowPeaks megadepth: xfun utils fs GenomicRanges readr cmdfun flowDensity: flowCore graphics flowViz car sp rgeos gplots RFOC flowWorkspace methods stats grDevices modeltools: stats stats4 methods adehabitatLT: sp methods ade4 adehabitatMA CircStats stats graphics grDevices utils proteinProfiles: graphics stats metafor: methods Matrix stats utils graphics grDevices nlme Mfuzz: Biobase e1071 tcltk tkWidgets pvac: affy stats Biobase tcltk2: tcltk HilbertVisGUI: HilbertVis GenomicFiles: methods BiocGenerics MatrixGenerics GenomicRanges SummarizedExperiment BiocParallel Rsamtools rtracklayer GenomicAlignments IRanges S4Vectors VariantAnnotation GenomeInfoDb brew: semisup: VGAM OnassisJavaLibs: rJava DirichletMultinomial: S4Vectors IRanges stats4 methods BiocGenerics Rcpi: stats utils methods RCurl rjson foreach doParallel Biostrings GOSemSim ChemmineR fmcsR rcdk seqLogo: methods grid stats4 grDevices powerTCR: cubature doParallel evmix foreach magrittr methods parallel purrr stats truncdist vegan VGAM TimiRGeN: Mfuzz MultiAssayExperiment biomaRt clusterProfiler dplyr FreqProf gtools gplots ggdendro gghighlight ggplot2 graphics grDevices igraph RCy3 readxl reshape2 rWikiPathways scales stats tidyr stringr PloGO2: GO.db GOstats lattice httr openxlsx xtable chromDraw: Rcpp GenomicRanges netprioR: methods graphics stats Matrix dplyr doParallel foreach parallel sparseMVN ggplot2 gridExtra pROC foreign: methods utils stats EDDA: Rcpp parallel methods ROCR DESeq baySeq snow edgeR graphics stats utils BiSeq: methods S4Vectors IRanges GenomicRanges SummarizedExperiment Formula BiocGenerics Biobase GenomeInfoDb rtracklayer parallel betareg lokern globaltest geuvPack: SummarizedExperiment RPostgres: bit64 blob DBI hms lubridate methods Rcpp withr plogr ADAMgui: stats utils methods ADAM GO.db dplyr shiny stringr stringi varhandle ggplot2 ggrepel ggpubr ggsignif reshape2 RColorBrewer colorRamps DT data.table gridExtra shinyjs knitr testthat ggplot2: digest glue grDevices grid gtable isoband MASS mgcv rlang scales stats tibble withr Rcpp: methods utils quantreg: stats SparseM methods graphics Matrix MatrixModels conquer artMS: AnnotationDbi biomaRt bit64 circlize cluster ComplexHeatmap corrplot data.table dplyr factoextra FactoMineR getopt ggdendro ggplot2 gplots ggrepel gProfileR graphics grDevices grid limma MSstats openxlsx org.Hs.eg.db org.Mm.eg.db PerformanceAnalytics pheatmap plotly plyr RColorBrewer scales seqinr stats stringr tidyr UpSetR utils VennDiagram yaml pd.mapping50k.hind240: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors tspair: Biobase LineagePulse: BiocParallel circlize compiler ComplexHeatmap ggplot2 gplots grDevices grid knitr Matrix methods RColorBrewer SingleCellExperiment splines stats SummarizedExperiment utils ccfindR: stats S4Vectors utils methods Matrix SummarizedExperiment SingleCellExperiment Rtsne graphics grDevices gtools RColorBrewer ape Rmpi irlba Rcpp Rdpack RcppEigen PoiClaClu: fcScan: stats plyr VariantAnnotation SummarizedExperiment rtracklayer GenomicRanges methods IRanges assertive.files: assertive.base assertive.numbers BeadDataPackR: stats utils lambda.r: formatR webdriver: callr base64enc curl debugme httr jsonlite R6 showimage utils withr agilp: PSICQUIC: methods IRanges biomaRt BiocGenerics httr plyr RCurl 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 BaalChIP: GenomicRanges IRanges Rsamtools GenomicAlignments GenomeInfoDb doParallel parallel doBy reshape2 scales coda foreach ggplot2 methods utils graphics stats pvca: Matrix Biobase vsn stats lme4 QuaternaryProd: Rcpp dplyr yaml ChemmineR: methods rjson graphics stats RCurl DBI digest BiocGenerics Rcpp ggplot2 grid gridExtra png base64enc DT rsvg BH CNORfuzzy: CellNOptR nloptr FANTOM3and4CAGE: EnMCB: foreach doParallel parallel stats survivalROC glmnet rms survivalsvm ggplot2 minfi IlluminaHumanMethylation450kanno.ilmn12.hg19 survival utils LIM: limSolve diagram motifcounter: Biostrings methods isva: qvalue fastICA JADE shinyMethylData: qualV: KernSmooth graphics grDevices stats utils minfiData: minfi IlluminaHumanMethylation450kmanifest IlluminaHumanMethylation450kanno.ilmn12.hg19 taRifx: reshape2 plyr GeneOverlap: stats RColorBrewer gplots methods origami: abind methods data.table assertthat future future.apply listenv cplm: coda Matrix splines methods biglm ggplot2 minqa nlme reshape2 statmod stats stats4 tweedie ldblock: methods Matrix snpStats VariantAnnotation GenomeInfoDb httr ensembldb EnsDb.Hsapiens.v75 Rsamtools GenomicFiles BiocGenerics NanoMethViz: methods ggplot2 S4Vectors SummarizedExperiment bsseq forcats assertthat AnnotationDbi Rcpp dplyr data.table e1071 fs GenomicRanges ggthemes glue patchwork purrr readr rlang RSQLite Rsamtools scales stats stringr tibble tidyr utils zlibbioc faahKO: xcms ENVISIONQuery: rJava XML utils kpmt: matrixStats stats methods utils httptest: testthat curl digest httr jsonlite stats utils fpc: MASS cluster mclust flexmix prabclus class diptest robustbase kernlab grDevices graphics methods stats utils parallel isomiRs: DiscriMiner SummarizedExperiment AnnotationDbi assertive.sets BiocGenerics Biobase broom cluster cowplot DEGreport DESeq2 IRanges dplyr GenomicRanges gplots ggplot2 gtools gridExtra grid grDevices graphics GGally limma methods RColorBrewer readr reshape rlang stats stringr S4Vectors tidyr tibble GeneBreak: QDNAseq CGHcall CGHbase GenomicRanges graphics methods stringr: glue magrittr stringi modelr: broom magrittr purrr rlang tibble tidyr tidyselect vctrs pillar: cli crayon ellipsis fansi lifecycle rlang utf8 utils vctrs brio: REBET: ASSET stats utils SQLDataFrame: dplyr dbplyr S4Vectors DBI lazyeval methods tools stats BiocGenerics RSQLite tibble rDGIdb: jsonlite httr methods graphics extrafontdb: MSGFplus: methods mzID ProtGenerics RegEnrich: S4Vectors dplyr tibble BiocSet SummarizedExperiment randomForest fgsea DOSE BiocParallel DESeq2 limma WGCNA ggplot2 methods reshape2 magrittr ggnewscale: ggplot2 cnvGSAdata: cnvGSA GeneStructureTools: Biostrings GenomicRanges IRanges data.table plyr stringdist stringr S4Vectors BSgenome.Mmusculus.UCSC.mm10 stats utils Gviz rtracklayer methods BiGGR: rsbml hyperdraw LIM stringr hypergraph limSolve ERSSA: edgeR DESeq2 ggplot2 RColorBrewer plyr BiocParallel grDevices stats utils hopach: cluster Biobase methods graphics grDevices stats utils BiocGenerics MCMCglmm: Matrix coda ape corpcor tensorA cubature methods chromstaRData: EnrichmentBrowser: SummarizedExperiment graph AnnotationDbi BiocFileCache BiocManager GSEABase GO.db KEGGREST KEGGgraph Rgraphviz S4Vectors SPIA edgeR graphite hwriter limma methods pathview safe wavClusteR: GenomicRanges Rsamtools methods BiocGenerics S4Vectors IRanges Biostrings foreach GenomicFeatures ggplot2 Hmisc mclust rtracklayer seqinr stringr AnnotationHub: BiocGenerics BiocFileCache utils methods grDevices RSQLite BiocManager BiocVersion curl rappdirs AnnotationDbi S4Vectors interactiveDisplayBase httr yaml dplyr plyranges: BiocGenerics IRanges GenomicRanges methods dplyr rlang magrittr tidyselect rtracklayer GenomicAlignments GenomeInfoDb Rsamtools S4Vectors utils GDSArray: gdsfmt methods BiocGenerics DelayedArray tools S4Vectors SNPRelate SeqArray diptest: graphics stats gam: stats splines foreach assertive.reflection: assertive.base utils DLBCL: Biobase stringi: tools utils stats gap: arrow: assertthat bit64 methods purrr R6 rlang stats tidyselect utils vctrs cpp11 CodeDepends: methods codetools graph XML utils flowBin: methods flowCore flowFP class limma snow BiocGenerics graphlayouts: igraph Rcpp RcppArmadillo VariantExperiment: S4Vectors SummarizedExperiment GenomicRanges GDSArray DelayedDataFrame tools utils stats methods gdsfmt SNPRelate SeqArray SeqVarTools DelayedArray Biostrings IRanges spqn: ggplot2 ggridges SummarizedExperiment BiocGenerics graphics stats utils matrixStats VariantTools: S4Vectors IRanges GenomicRanges VariantAnnotation methods Rsamtools BiocGenerics Biostrings parallel GenomicFeatures Matrix rtracklayer BiocParallel GenomeInfoDb BSgenome Biobase MBASED: RUnit BiocGenerics BiocParallel GenomicRanges SummarizedExperiment seqinr: ade4 segmented highr: xfun GSEAmining: dplyr tidytext dendextend tibble ggplot2 ggwordcloud stringr gridExtra rlang grDevices graphics stats methods nortest: stats CancerSubtypes: sigclust NMF SNFtool iCluster cluster impute limma ConsensusClusterPlus grDevices survival gbm: lattice parallel survival filematrix: methods utils Cubist: lattice reshape2 utils TxDb.Athaliana.BioMart.plantsmart22: GenomicFeatures AnnotationDbi diffobj: crayon tools methods utils stats scMerge: BiocParallel BiocSingular cluster DelayedArray DelayedMatrixStats distr igraph M3Drop parallel pdist proxy ruv S4Vectors SingleCellExperiment SummarizedExperiment rfaRm: httr stringi rsvg magick data.table Biostrings utils rvest xml2 IRanges S4Vectors VennDiagram: grid futile.logger GSgalgoR: cluster doParallel foreach matchingR nsga2R survival proxy stats methods QUBIC: biclust Rcpp methods Matrix RcppArmadillo FRASER: BiocParallel data.table Rsamtools SummarizedExperiment AnnotationDbi BBmisc Biobase BiocGenerics biomaRt BSgenome cowplot DelayedArray DelayedMatrixStats extraDistr generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges grDevices ggplot2 ggrepel HDF5Array matrixStats methods OUTRIDER pcaMethods pheatmap plotly PRROC RColorBrewer rhdf5 Rsubread R.utils S4Vectors stats tibble tools utils VGAM Rcpp RcppArmadillo esquisse: datamods rstudioapi shiny htmltools jsonlite shinyWidgets ggplot2 scales rlang grDevices styler hapFabia: Biobase fabia methods graphics grDevices stats utils MCbiclust: BiocParallel graphics utils stats AnnotationDbi GO.db org.Hs.eg.db GGally ggplot2 scales cluster WGCNA svgPanZoom: htmlwidgets hgu133plus2cdf: utils AnnotationDbi DrImpute: Rcpp RcppArmadillo fst: Rcpp EBImage: methods BiocGenerics graphics grDevices stats abind tiff jpeg png locfit fftwtools utils htmltools htmlwidgets RCurl SIFT.Hsapiens.dbSNP132: VariantAnnotation RSQLite AnnotationDbi abseqR: ggplot2 RColorBrewer circlize reshape2 VennDiagram plyr flexdashboard BiocParallel png grid gridExtra rmarkdown knitr vegan ggcorrplot ggdendro plotly BiocStyle stringr utils methods grDevices stats tools graphics signal: MASS graphics grDevices stats utils bioCancer: radiant.data cgdsr XML shiny AlgDesign import methods shinythemes Biobase geNetClassifier AnnotationFuncs org.Hs.eg.db DOSE clusterProfiler reactome.db ReactomePA DiagrammeR visNetwork htmlwidgets plyr tibble DT dplyr Rcwl: yaml methods S4Vectors utils stats BiocParallel batchtools DiagrammeR shiny R.utils codetools PCAtools: ggplot2 ggrepel lattice grDevices cowplot methods reshape2 stats Matrix DelayedMatrixStats DelayedArray BiocSingular BiocParallel Rcpp dqrng beachmat BH brainflowprobes: Biostrings BSgenome.Hsapiens.UCSC.hg19 bumphunter cowplot derfinder derfinderPlot GenomicRanges ggplot2 RColorBrewer utils grDevices GenomicState SIAMCAT: mlr phyloseq beanplot glmnet graphics grDevices grid gridBase gridExtra LiblineaR matrixStats methods ParamHelpers pROC PRROC RColorBrewer scales stats stringr utils infotheo progress corrplot afex: lme4 pbkrtest lmerTest car reshape2 stats methods utils libcoin: stats mvtnorm Anaquin: ggplot2 ROCR knitr qvalue locfit methods stats utils plyr DESeq2 SIFT.Hsapiens.dbSNP137: VariantAnnotation RSQLite AnnotationDbi matrixStats: styler: backports cli magrittr purrr R.cache rematch2 rlang rprojroot tibble tools withr xfun CAGEr: methods MultiAssayExperiment beanplot BiocGenerics BiocParallel BSgenome data.table DelayedArray formula.tools GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges KernSmooth memoise plyr Rsamtools reshape rtracklayer S4Vectors som stringdist stringi SummarizedExperiment utils vegan VGAM drtmle: SuperLearner np future doFuture future.apply future.batchtools HardyWeinberg: mice Rsolnp Rcpp genomationData: DRaWR: Matrix ROCR gtools: methods stats utils colourpicker: ggplot2 htmltools htmlwidgets jsonlite miniUI shiny shinyjs utils iGC: plyr data.table timeDate: graphics utils stats methods qwraps2: dplyr ggplot2 knitr Rcpp rlang utils xfun RcppArmadillo SpikeInSubset: Biobase affy cancerclass: Biobase binom methods stats prebsdata: plsgenomics: MASS boot parallel reshape2 plyr fields RhpcBLASctl MeSH.Aca.eg.db: MeSHDbi Melissa: BPRMeth GenomicRanges data.table parallel ROCR matrixcalc mclust ggplot2 doParallel foreach MCMCpack cowplot magrittr mvtnorm truncnorm assertthat BiocStyle stats utils affy: BiocGenerics Biobase affyio BiocManager graphics grDevices methods preprocessCore stats utils zlibbioc LPE: stats FMStable: SummarizedBenchmark: tidyr SummarizedExperiment S4Vectors BiocGenerics methods UpSetR rlang stringr utils BiocParallel ggplot2 mclust dplyr digest sessioninfo crayon tibble smatr: datasets: flowFitExampleData: flowCore methods expint: gdata: gtools stats methods utils airway: SummarizedExperiment Hmisc: lattice survival Formula ggplot2 methods latticeExtra cluster rpart nnet foreign gtable grid gridExtra data.table htmlTable viridis htmltools base64enc trigger: corpcor qtl qvalue methods graphics sva gargle: cli fs glue httr jsonlite rappdirs rlang rstudioapi stats withr iterators: utils randomizr: methVisual: Biostrings plotrix gsubfn grid sqldf ca graphics grDevices gridBase IRanges stats utils RankProd: stats methods Rmpfr gmp graphics objectSignals: methods signeR: VariantAnnotation NMF BiocGenerics Biostrings class graphics grDevices GenomeInfoDb GenomicRanges IRanges nloptr methods stats utils PMCMR Rcpp RcppArmadillo MSPrep: SummarizedExperiment S4Vectors pcaMethods VIM crmn preprocessCore sva dplyr tidyr tibble magrittr rlang stats stringr methods ddpcr HCABrowser: dplyr AnVIL BiocFileCache googleAuthR httr methods readr rlang utils GENESIS: Biobase BiocGenerics GWASTools gdsfmt GenomicRanges IRanges S4Vectors SeqArray SeqVarTools SNPRelate data.table foreach graphics grDevices igraph Matrix methods reshape2 stats utils derfinder: BiocGenerics AnnotationDbi BiocParallel bumphunter derfinderHelper GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges methods qvalue Rsamtools rtracklayer S4Vectors stats utils precrec: Rcpp ggplot2 assertthat grid gridExtra methods data.table withr genefilter: BiocGenerics AnnotationDbi annotate Biobase graphics methods stats survival prognosticROC: splines survival MultiDataSet: Biobase BiocGenerics GenomicRanges IRanges S4Vectors SummarizedExperiment methods utils ggplot2 ggrepel qqman limma KEGGdzPathwaysGEO: Biobase BiocGenerics OLINgui: OLIN graphics marray tcltk tkWidgets widgetTools TENxBrainData: SingleCellExperiment HDF5Array AnnotationHub ExperimentHub ggalluvial: ggplot2 stats dplyr tidyr lazyeval rlang tidyselect pdInfoBuilder: methods Biobase RSQLite affxparser oligo Biostrings BiocGenerics DBI IRanges oligoClasses S4Vectors MBA: BH rstan: StanHeaders ggplot2 methods stats4 inline gridExtra Rcpp RcppParallel loo pkgbuild withr V8 RcppEigen BH HiTC: methods IRanges GenomicRanges Biostrings graphics grDevices rtracklayer RColorBrewer Matrix parallel GenomeInfoDb HiCBricks: utils curl rhdf5 R6 grid ggplot2 viridis RColorBrewer scales reshape2 stringr data.table GenomeInfoDb GenomicRanges stats IRanges grDevices S4Vectors digest tibble jsonlite BiocParallel R.utils readr methods rqubic: methods Biobase BiocGenerics biclust occugene: seqcombo: Biostrings cowplot dplyr ggplot2 grid igraph magrittr methods rvcheck utils AffyExpress: affy limma capushe: methods graphics MASS pkgload: cli crayon desc methods rlang rprojroot rstudioapi utils withr elasticnet: lars ggm: igraph methods graph biocViews: Biobase graph methods RBGL tools utils XML RCurl RUnit BiocManager hipathia: igraph AnnotationHub MultiAssayExperiment SummarizedExperiment coin stats limma grDevices utils graphics preprocessCore servr DelayedArray matrixStats methods S4Vectors DECIPHER: Biostrings RSQLite stats parallel methods DBI S4Vectors IRanges XVector FCBF: ggplot2 gridExtra pbapply parallel SummarizedExperiment stats mclust ExploreModelMatrix: shiny shinydashboard DT cowplot utils dplyr magrittr tidyr ggplot2 stats methods rintrojs scales tibble MASS limma S4Vectors shinyjs truncdist: stats4 evd GOstats: Biobase Category graph methods stats stats4 AnnotationDbi GO.db RBGL annotate AnnotationForge Rgraphviz readbitmap: bmp jpeg png tiff countsimQC: rmarkdown edgeR DESeq2 dplyr tidyr ggplot2 grDevices tools SummarizedExperiment genefilter DT GenomeInfoDbData caTools randtests stats utils methods LSD: scde: flexmix Rcpp RcppArmadillo mgcv Rook rjson MASS Cairo RColorBrewer edgeR quantreg methods nnet RMTstat extRemes pcaMethods BiocParallel parallel MmPalateMiRNA: methods Biobase xtable limma statmod lattice vsn trust: stats longitudinal: corpcor graphics grDevices stats SWATH2stats: data.table reshape2 ggplot2 stats grDevices graphics utils biomaRt methods signet: graph igraph RBGL graphics utils stats methods echarts4r: htmlwidgets magrittr dplyr purrr countrycode broom shiny scales corrplot htmltools jsonlite rstudioapi SingleCellExperiment: SummarizedExperiment methods utils stats S4Vectors BiocGenerics MCL: expm RepViz: GenomicRanges Rsamtools IRanges biomaRt S4Vectors graphics grDevices utils zeallot: CONFESSdata: RNASeqPower: EnrichedHeatmap: methods grid ComplexHeatmap GenomicRanges matrixStats stats GetoptLong Rcpp utils locfit circlize IRanges pwOmics: data.table rBiopaxParser igraph STRINGdb graphics gplots Biobase BiocGenerics AnnotationDbi biomaRt AnnotationHub GenomicRanges graph grDevices stats utils rrBLUP: stats graphics grDevices scds: Matrix S4Vectors SingleCellExperiment SummarizedExperiment xgboost methods stats dplyr pROC simpIntLists: SNAGEE: SNAGEEdata openPrimeRui: openPrimeR shiny shinyjs shinyBS DT rmarkdown ddpcr: DT dplyr ggplot2 lazyeval magrittr mixtools plyr readr shiny shinyjs tibble nloptr: triebeard: Rcpp doppelgangR: Biobase BiocParallel sva impute digest mnormt methods grDevices graphics stats SummarizedExperiment utils MEAL: Biobase MultiDataSet GenomicRanges limma vegan BiocGenerics minfi IRanges S4Vectors methods parallel ggplot2 permute Gviz missMethyl isva SummarizedExperiment SmartSVA graphics stats utils matrixStats CRISPRseek: BiocGenerics Biostrings parallel data.table seqinr S4Vectors IRanges BSgenome BiocParallel hash methods reticulate rhdf5 bench: glue methods pillar profmem rlang stats tibble utils BadRegionFinder: VariantAnnotation Rsamtools biomaRt GenomicRanges S4Vectors utils stats grDevices graphics cleaver: methods Biostrings S4Vectors IRanges BrainStars: RCurl Biobase methods RJSONIO crisprseekplus: shiny shinyjs CRISPRseek DT utils GUIDEseq GenomicRanges GenomicFeatures BiocManager BSgenome AnnotationDbi hash MEB: e1071 SummarizedExperiment crosstalk: htmltools jsonlite lazyeval R6 MEAT: impute dynamicTreeCut glmnet grDevices graphics stats utils stringr tibble RPMM minfi dplyr SummarizedExperiment wateRmelon R4RNA: Biostrings TxDb.Rnorvegicus.UCSC.rn4.ensGene: GenomicFeatures AnnotationDbi KMsurv: cogena: cluster ggplot2 kohonen methods class gplots mclust amap apcluster foreach parallel doParallel fastcluster corrplot biwt Biobase reshape2 stringr tibble tidyr dplyr devtools Pviz: Gviz biovizBase Biostrings GenomicRanges IRanges data.table methods nlcv: a4Core MLInterfaces xtable limma MASS methods graphics Biobase multtest RColorBrewer pamr randomForest ROCR ipred e1071 kernlab Path2PPI: igraph methods TreeAndLeaf: RedeR igraph ape methods R2WinBUGS: coda boot utils stats graphics DRIMSeq: utils stats MASS GenomicRanges IRanges S4Vectors BiocGenerics methods BiocParallel limma edgeR ggplot2 reshape2 MMDiffBamSubset: RColorBrewer: IlluminaHumanMethylation450kanno.ilmn12.hg19: minfi SCAN.UPC: Biobase oligo Biostrings GEOquery affy affyio foreach sva utils methods MASS tools IRanges INPower: mvtnorm pumadata: Biobase puma oligo TFutils: methods dplyr magrittr miniUI shiny Rsamtools GSEABase rjson BiocFileCache DT httr readxl BSgenome.Mmusculus.UCSC.mm10.masked: BSgenome BSgenome.Mmusculus.UCSC.mm10 Category: methods stats4 BiocGenerics AnnotationDbi Biobase Matrix utils stats graph RBGL GSEABase genefilter annotate DBI fastcluster: SNPlocs.Hsapiens.dbSNP.20101109: IRanges GenomicRanges methods S4Vectors mlbench: Rcade: methods GenomicRanges Rsamtools baySeq utils grDevices stats graphics rgl plotrix S4Vectors IRanges GenomeInfoDb GenomicAlignments Delaporte: stats DiffBind: GenomicRanges SummarizedExperiment RColorBrewer amap gplots grDevices limma GenomicAlignments locfit stats utils IRanges lattice systemPipeR tools Rcpp dplyr ggplot2 BiocParallel parallel S4Vectors Rsamtools DESeq2 methods graphics ggrepel apeglm ashr GreyListChIP Rhtslib devtools: usethis callr cli desc ellipsis fs httr lifecycle memoise pkgbuild pkgload rcmdcheck remotes rlang roxygen2 rstudioapi rversions sessioninfo stats testthat tools utils withr ELBOW: graphics stats utils visNetwork: htmlwidgets htmltools jsonlite magrittr utils methods grDevices stats gld: stats graphics e1071 lmom benchmarkmeData: dplyr graphics tibble utils RTopper: Biobase limma multtest chimera: Biobase GenomicRanges Rsamtools GenomicAlignments methods AnnotationDbi BSgenome.Hsapiens.UCSC.hg19 TxDb.Hsapiens.UCSC.hg19.knownGene Homo.sapiens spacetime: graphics utils stats methods lattice sp zoo xts intervals debugme: crayon grDevices limmaGUI: methods grDevices graphics limma R2HTML tcltk tkrplot xtable utils Rnits: Biobase ggplot2 limma methods affy boot impute splines graphics qvalue reshape2 fresh: sass htmltools shiny rstudioapi haven: forcats hms methods readr rlang tibble tidyselect vctrs cpp11 SigCheck: MLInterfaces Biobase e1071 BiocParallel survival graphics stats utils methods tmvtnorm: mvtnorm utils Matrix stats4 gmm stats methods ggfittext: grid stringi ggplot2 shades parody: tools utils aplpack: gdsfmt: methods MDTS: GenomicAlignments GenomicRanges IRanges Biostrings DNAcopy Rsamtools parallel stringr ClusterR: gtools Rcpp graphics grDevices utils stats gmp ggplot2 RcppArmadillo ExperimentHubData: utils BiocGenerics S4Vectors AnnotationHubData methods ExperimentHub BiocManager DBI BiocCheck httr curl biocViews graph rbokeh: htmlwidgets maps methods jsonlite digest hexbin lazyeval pryr magrittr ggplot2 scales gistr kissDE: aod Biobase DESeq2 DSS ggplot2 gplots graphics grDevices matrixStats stats utils foreach doParallel parallel rebus.unicode: rebus.base TRONCO: bnlearn Rgraphviz gtools parallel foreach doParallel iterators RColorBrewer circlize cgdsr igraph grid gridExtra xtable gtable scales R.matlab grDevices graphics stats utils methods PWMEnrich.Dmelanogaster.background: methods PWMEnrich BSgenome.Celegans.UCSC.ce10: BSgenome gmm: sandwich stats methods grDevices graphics BSgenome.Celegans.UCSC.ce11: BSgenome Prostar: DAPAR DAPARdata rhandsontable data.table shinyjs DT shiny shinyBS shinyAce highcharter htmlwidgets webshot R.utils shinythemes XML later rclipboard shinycssloaders future promises colourpicker BiocManager shinyjqui shinyTree shinyWidgets sass tibble TitanCNA: BiocGenerics IRanges GenomicRanges VariantAnnotation foreach GenomeInfoDb data.table dplyr phyloseq: ade4 ape Biobase BiocGenerics biomformat Biostrings cluster data.table foreach ggplot2 igraph methods multtest plyr reshape2 scales vegan gmp: methods goProfiles: Biobase AnnotationDbi GO.db CompQuadForm stringr NCmisc: grDevices graphics stats utils tools proftools methods bigmemory: methods Rcpp utils bigmemory.sri BH topologyGSA: graph gRbase qpgraph fields methods howmany: graphics stats SPsimSeq: stats methods SingleCellExperiment fitdistrplus graphics edgeR Hmisc WGCNA limma mvtnorm phyloseq utils BiocCaseStudies: tools methods utils Biobase PtH2O2lipids: xcms CAMERA LOBSTAHS methods utils class: stats utils MASS MACPET: InteractionSet bigmemory BH Rcpp intervals plyr Rsamtools stats utils methods GenomicRanges S4Vectors IRanges GenomeInfoDb gtools GenomicAlignments knitr rtracklayer BiocParallel Rbowtie GEOquery Biostrings ShortRead futile.logger TargetSearchData: MMUPHin: Maaslin2 metafor fpc igraph ggplot2 dplyr tidyr cowplot utils stats grDevices flowStats: BiocGenerics MASS flowCore flowWorkspace ncdfFlow flowViz fda Biobase methods grDevices graphics stats cluster utils KernSmooth lattice ks RColorBrewer rrcov preprocessCore: stats SharedObject: Rcpp methods stats BiocGenerics BH lokern: grDevices graphics stats utils sfsmisc sapFinder: rTANDEM pheatmap Rcpp graphics grDevices stats utils gnm: graphics grDevices MASS Matrix methods nnet qvcalc relimp stats utils aroma.apd: R.methodsS3 R.oo R.utils R.huge grImport2: methods grDevices grid XML png jpeg base64enc ggmcmc: dplyr tidyr ggplot2 GGally kohonen: Rcpp mixsmsn: mvtnorm gcrma: affy graphics methods stats utils Biobase affyio XVector Biostrings splines BiocManager LinkHD: methods ggplot2 stats scales cluster graphics ggpubr gridExtra vegan rio MultiAssayExperiment emmeans reshape2 data.table illuminaHumanv3.db: methods AnnotationDbi org.Hs.eg.db SnowballC: genalg: memoise: rlang cachem shinyalert: htmltools shiny stats uuid diggit: Biobase methods ks viper parallel MSstats: lme4 marray limma gplots ggplot2 methods grid ggrepel preprocessCore reshape2 survival statmod minpack.lm utils grDevices graphics stats doSNOW snow foreach data.table MASS dplyr tidyr broom purrr stringr vcd: grid stats utils MASS grDevices colorspace lmtest ChIPXpressData: bigmemory AnVILBilling: methods DT shiny bigrquery shinytoastr DBI magrittr dplyr lubridate plotly ggplot2 scatterplot3d: grDevices graphics stats rARPACK: RSpectra msd16s: Biobase metagenomeSeq GenomicOZone: Ckmeans.1d.dp GenomicRanges biomaRt ggplot2 grDevices stats utils plyr gridExtra lsr parallel ggbio S4Vectors IRanges GenomeInfoDb Rdpack bs4Dash: shiny htmltools magrittr: methylMnM: edgeR statmod variancePartition: ggplot2 limma BiocParallel scales Biobase methods MASS pbkrtest lmerTest iterators splines foreach doParallel colorRamps gplots progress reshape2 lme4 grDevices graphics utils stats labeling: stats graphics bcellViper: Biobase methods skewr: methylumi wateRmelon mixsmsn IlluminaHumanMethylation450kmanifest minfi S4Vectors RColorBrewer lpNet: lpSolve mnem: cluster graph Rgraphviz flexclust lattice naturalsort snowfall stats4 tsne methods graphics stats utils Linnorm data.table Rcpp RcppEigen matrixStats grDevices e1071 SQUADD: graphics grDevices methods RColorBrewer stats utils DMRcaller: GenomicRanges IRanges S4Vectors parallel Rcpp RcppRoll betareg grDevices graphics methods stats utils sonicLength: splines CCPROMISE: stats methods CCP PROMISE Biobase GSEABase utils countrycode: gramm4R: basicTrendline investr minerva psych grDevices graphics stats DelayedArray SummarizedExperiment DMwR phyloseq RGMQL: RGMQLlib httr rJava GenomicRanges rtracklayer data.table utils plyr xml2 methods S4Vectors dplyr stats glue BiocGenerics BBmisc: utils methods stats checkmate googlesheets4: cellranger curl gargle glue googledrive httr ids lifecycle magrittr methods purrr rematch2 rlang tibble utils vctrs Affyhgu133A2Expr: rrvgo: GOSemSim AnnotationDbi GO.db pheatmap ggplot2 ggrepel treemap tm wordcloud shiny grDevices grid stats methods iCluster: lattice caTools gdata gtools gplots parallel dendextend: utils stats datasets magrittr ggplot2 viridis vctrs: ellipsis glue rlang pkgconfig: utils ReQON: Rsamtools seqbias rJava graphics stats utils grDevices mixOmics: MASS lattice ggplot2 igraph ellipse corpcor RColorBrewer parallel dplyr tidyr reshape2 methods matrixStats rARPACK gridExtra grDevices graphics stats ggrepel BiocParallel utils IsoGene: Iso xtable Biobase affy ff tcltk dupRadar: Rsubread tRNAscanImport: GenomicRanges tRNA methods stringr BiocGenerics Biostrings Structstrings S4Vectors IRanges XVector GenomeInfoDb rtracklayer BSgenome Rsamtools biomaRt: methods utils XML AnnotationDbi progress stringr httr openssl BiocFileCache rappdirs xml2 SQUAREM: locfdr: stats splines graphics myvariant: VariantAnnotation httr jsonlite S4Vectors Hmisc plyr magrittr GenomeInfoDb Rbowtie2: GEWIST: car MLP: AnnotationDbi affy plotrix gplots gmodels gdata gtools RMySQL: DBI methods ICSNP: mvtnorm ICS clusterExperiment: SingleCellExperiment SummarizedExperiment BiocGenerics methods NMF RColorBrewer ape cluster stats limma howmany locfdr matrixStats graphics parallel RSpectra kernlab stringr S4Vectors grDevices DelayedArray HDF5Array Matrix Rcpp edgeR scales zinbwave phylobase pracma mbkmeans KEGGREST: methods httr png Biostrings TCGAbiolinksGUI.data: logistf: mice mgcv formula.tools chopsticks: graphics stats utils methods survival flowClust: BiocGenerics methods Biobase graph ellipse flowViz flowCore clue corpcor mnormt parallel basilisk: utils methods parallel reticulate filelock basilisk.utils readJDX: stringr cosmiq: Rcpp pracma xcms MassSpecWavelet faahKO SamSPECTRAL: methods pasilla: fGarch: timeDate timeSeries fBasics fastICA Matrix graphics methods stats utils ORIClust: leaps: gsl: evmix: stats graphics MASS splines gsl SparseM grDevices pulsedSilac: robustbase methods R.utils taRifx S4Vectors SummarizedExperiment ggplot2 ggridges stats utils UpSetR cowplot grid MuMIn RcppAnnoy: methods Rcpp CHRONOS: XML RCurl RBGL parallel foreach doParallel openxlsx igraph circlize graph stats utils grDevices graphics methods biomaRt rJava nlme: graphics stats utils lattice gss: stats logging: methods htmlTable: stringr knitr magrittr methods checkmate htmlwidgets htmltools rstudioapi SigFuge: GenomicRanges ggplot2 matlab reshape sigclust metagene: R6 GenomicRanges BiocParallel rtracklayer gplots tools GenomicAlignments GenomeInfoDb GenomicFeatures IRanges ggplot2 muStat Rsamtools DBChIP matrixStats purrr data.table magrittr methods utils ensembldb EnsDb.Hsapiens.v86 stringr biglm: DBI methods cicerone: R6 shiny assertthat metagenomeSeq: Biobase limma glmnet methods RColorBrewer parallel matrixStats foreach Matrix gplots graphics grDevices stats utils Wrench TFARM: arules fields GenomicRanges graphics stringr methods stats gplots NeighborNet: methods graph stats NanoporeRNASeq: ExperimentHub plotrix: grDevices graphics stats utils bodymapRat: SummarizedExperiment ExperimentHub utils GAPGOM: stats utils methods Matrix fastmatch plyr dplyr magrittr data.table igraph graph RBGL GO.db org.Hs.eg.db org.Mm.eg.db GOSemSim GEOquery AnnotationDbi Biobase BiocFileCache matrixStats maigesPack: convert graph limma marray methods lars: biosigner: Biobase ropls methods e1071 MultiDataSet randomForest doFuture: foreach future globals iterators parallel utils GARS: ggplot2 cluster DaMiRseq MLSeq stats methods SummarizedExperiment gsean: fgsea PPInfer kappalab: methods lpSolve quadprog kernlab ontoProc: ontologyIndex Biobase S4Vectors methods AnnotationDbi stats utils BiocFileCache shiny graph Rgraphviz ontologyPlot dplyr magrittr DT igraph badger: dlstats rvcheck desc usethis dagLogo: methods grid pheatmap Biostrings UniProt.ws BiocGenerics utils biomaRt motifStack paxtoolsr: rJava methods XML utils httr igraph plyr rjson R.utils jsonlite readr subspace: ggvis colorspace stringr rJava MSEADbi: methods stats utils AnnotationDbi RSQLite DBI Biobase GO.db: methods AnnotationDbi MSQC: graphics stats utils rgl RTNduals: RTN methods graphics grDevices stats utils HEEBOdata: ORFik: IRanges GenomicRanges GenomicAlignments S4Vectors GenomeInfoDb GenomicFeatures AnnotationDbi rtracklayer Rcpp data.table Biostrings biomartr BiocGenerics BiocParallel BSgenome DESeq2 ggplot2 gridExtra cowplot GGally methods R.utils RCurl Rsamtools utils stats SummarizedExperiment fst xml2 tools hgu133acdf: utils AnnotationDbi bigmemory.sri: methods PANTHER.db: AnnotationDbi AnnotationHub utils methods RSQLite BiocFileCache seq2pathway.data: scClassify: S4Vectors limma ggraph igraph methods cluster minpack.lm mixtools BiocParallel proxy proxyC Matrix ggplot2 hopach diptest mgcv stats graphics statmod scsR: STRINGdb methods BiocGenerics Biostrings IRanges plyr tcltk sqldf hash ggplot2 graphics grDevices RColorBrewer multiGSEA: magrittr graphite AnnotationDbi dplyr fgsea metap rappdirs rlang methods picante: ape vegan nlme methods RNAsense: ggplot2 parallel NBPSeq qvalue SummarizedExperiment stats utils methods InterMineR: Biostrings RCurl XML xml2 RJSONIO sqldf igraph httr S4Vectors IRanges GenomicRanges SummarizedExperiment methods Affymoe4302Expr: LOBSTAHS: xcms CAMERA methods utils goftest: stats rTANDEM: XML Rcpp data.table methods bootstrap: stats OMICsPCAdata: MultiAssayExperiment nls2: proto nucleR: methods Biobase BiocGenerics Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors ShortRead dplyr ggplot2 magrittr parallel stats utils grDevices docopt: methods vulcandata: utils ClassifyR: methods S4Vectors MultiAssayExperiment BiocParallel locfit grid utils plyr ddCt: methods Biobase RColorBrewer xtable lattice BiocGenerics netboxr: igraph parallel RColorBrewer DT stats clusterProfiler data.table gplots jsonlite plyr COMPoissonReg: stats Rcpp MeSH.PCR.db: MeSHDbi exomePeak2: SummarizedExperiment cqn Rsamtools GenomicAlignments GenomicRanges GenomicFeatures DESeq2 ggplot2 mclust genefilter Biostrings BSgenome BiocParallel IRanges S4Vectors reshape2 rtracklayer apeglm methods stats utils Biobase GenomeInfoDb locfit: lattice renv: utils geneplast.data.string.v91: rRDPData: rRDP AffyCompatible: XML RCurl methods Biostrings restfulSE: SummarizedExperiment DelayedArray utils stats methods S4Vectors Biobase reshape2 AnnotationDbi DBI GO.db rhdf5client dplyr magrittr bigrquery ExperimentHub AnnotationHub rlang lava: grDevices graphics methods numDeriv stats survival SQUAREM utils RTCGA.methylation: RTCGA scry: stats methods DelayedArray glmpca HDF5Array Matrix SingleCellExperiment SummarizedExperiment BiocSingular golem: attempt cli config crayon desc dockerfiler fs here htmltools jsonlite pkgload remotes rlang roxygen2 rstudioapi shiny testthat usethis utils yaml statnet.common: utils methods coda parallel tools rle Rlabkey: httr jsonlite Rcpp 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 QDNAseq: graphics methods stats utils Biobase CGHbase CGHcall DNAcopy GenomicRanges IRanges matrixStats R.utils Rsamtools future future.apply CorMut: methods seqinr igraph GlobalOptions: methods utils explorase: limma rggobi RGtk2 EBSeq: blockmodeling gplots testthat aricode: Matrix Rcpp CrispRVariants: ggplot2 AnnotationDbi BiocParallel Biostrings methods GenomeInfoDb GenomicAlignments GenomicRanges grDevices grid gridExtra IRanges reshape2 Rsamtools S4Vectors utils repo: digest tools nipals: nethet: glasso mvtnorm GeneNet huge CompQuadForm ggm mclust parallel GSA limma multtest ICSNP glmnet network ggplot2 grDevices graphics stats utils GraphAT: graph methods MCMCpack stats rlecuyer: estrogen: topGO: methods BiocGenerics graph Biobase GO.db AnnotationDbi SparseM lattice matrixStats DBI excelR: htmlwidgets jsonlite IMAS: GenomicFeatures ggplot2 IVAS doParallel lme4 BiocGenerics GenomicRanges IRanges foreach AnnotationDbi S4Vectors GenomeInfoDb stats ggfortify grDevices methods Matrix utils graphics gridExtra grid lattice Rsamtools survival BiocParallel GenomicAlignments parallel ALPS: assertthat BiocParallel ChIPseeker corrplot data.table dplyr GenomicRanges GGally genefilter gghalves ggplot2 ggseqlogo Gviz magrittr org.Hs.eg.db plyr reshape2 rtracklayer stats stringr tibble tidyr TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene utils SPLINTER: grDevices stats graphics ggplot2 seqLogo Biostrings biomaRt GenomicAlignments GenomicRanges GenomicFeatures Gviz IRanges S4Vectors GenomeInfoDb utils plyr stringr methods BSgenome.Mmusculus.UCSC.mm9 googleVis netSmooth: scater clusterExperiment entropy SummarizedExperiment SingleCellExperiment Matrix cluster data.table stats methods DelayedArray HDF5Array flexdashboard: tools jsonlite htmltools knitr htmlwidgets rmarkdown shiny affyILM: methods gcrma affxparser affy graphics Biobase TargetSearch: ncdf4 graphics grDevices methods stats utils assertthat TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts: GenomicFeatures AnnotationDbi motifStack: methods grid ade4 Biostrings ggplot2 grDevices graphics htmlwidgets stats stats4 utils XML ASSET: MASS msm rmeta iteremoval: ggplot2 magrittr graphics utils GenomicRanges SummarizedExperiment GeneNet: corpcor longitudinal fdrtool stats grDevices dplR: graphics grDevices grid stats utils lattice Matrix digest matrixStats png R.utils stringi stringr XML plyr signal snapcount: R6 httr rlang purrr jsonlite assertthat data.table Matrix magrittr methods stringr stats IRanges GenomicRanges SummarizedExperiment rebus: rebus.base rebus.datetimes rebus.numbers rebus.unicode rsvd: Matrix CexoR: S4Vectors IRanges Rsamtools GenomeInfoDb GenomicRanges rtracklayer idr RColorBrewer genomation BgeeCall: GenomicFeatures rhdf5 tximport Biostrings rtracklayer biomaRt jsonlite methods grDevices graphics stats utils rslurm rsvg: ctsGE: ccaPP ggplot2 limma reshape2 shiny stats stringr utils outliers: FlowSorted.Blood.450k: minfi multcomp: stats graphics mvtnorm survival TH.data sandwich codetools flowCyBar: gplots vegan methods pickgene: graphics grDevices MASS stats utils COSINE: MASS genalg scattermore: ggplot2 scales grid grDevices graphics miRBaseVersions.db: AnnotationDbi DBI RSQLite methods gtools TAPseq: methods GenomicAlignments GenomicRanges IRanges BiocGenerics S4Vectors GenomeInfoDb BSgenome GenomicFeatures Biostrings dplyr tidyr BiocParallel ChIPQC: ggplot2 DiffBind GenomicRanges BiocGenerics S4Vectors IRanges Rsamtools GenomicAlignments chipseq gtools BiocParallel 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 cellTree: topGO topicmodels slam maptpx igraph xtable gplots SIMD: edgeR statmod methylMnM stats utils miRNApath: methods hunspell: Rcpp digest gganimate: ggplot2 stringi tweenr grid rlang glue progress plyr scales grDevices utils RcppZiggurat: Rcpp parallel graphics stats utils RcppGSL RefPlus: Biobase affy affyPLM preprocessCore cBioPortalData: AnVIL MultiAssayExperiment BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges methods readr RaggedExperiment RTCGAToolbox S4Vectors SummarizedExperiment stats tibble tidyr TCGAutils utils methylInheritance: methylKit BiocParallel GenomicRanges IRanges S4Vectors methods parallel ggplot2 gridExtra rebus IsoCorrectoR: dplyr magrittr methods quadprog readr readxl stringr tibble tools utils pracma WriteXLS PMCMR: stats base protViz: methods Rcpp GENLIB: Rcpp kinship2 methods bootstrap Matrix lattice quadprog foreach parallel doParallel nondetects: Biobase limma mvtnorm utils methods arm HTqPCR alabama: numDeriv adSplit: methods AnnotationDbi Biobase cluster GO.db graphics grDevices KEGG.db multtest stats gmapR: methods GenomeInfoDb GenomicRanges Rsamtools S4Vectors IRanges BiocGenerics rtracklayer GenomicFeatures Biostrings VariantAnnotation tools Biobase BSgenome GenomicAlignments BiocParallel waiter: R6 shiny crayon magrittr htmltools LoomExperiment: S4Vectors SingleCellExperiment SummarizedExperiment methods rhdf5 rtracklayer DelayedArray GenomicRanges HDF5Array Matrix stats stringr utils MESS: MASS Matrix Rcpp geepack geeM ggplot2 ggformula glmnet kinship2 methods mvtnorm parallel RcppArmadillo FlowSOM: igraph stats utils flowCore ConsensusClusterPlus BiocGenerics tsne CytoML flowWorkspace XML RColorBrewer SwimR: methods gplots heatmap.plus signal R2HTML GenRank: matrixStats reshape2 survcomp progress: hms prettyunits R6 crayon seqminer: GOfuncR: vioplot Rcpp mapplots gtools GenomicRanges IRanges AnnotationDbi utils grDevices graphics stats DO.db: methods AnnotationDbi BiocCheck: biocViews BiocManager stringdist graph httr tools optparse codetools methods utils knitr EpiDISH: MASS e1071 quadprog parallel stats matrixStats stringr locfdr Matrix Lmoments: stats Rcpp RcppArmadillo ivygapSE: SummarizedExperiment shiny survival survminer hwriter plotly ggplot2 S4Vectors graphics stats utils UpSetR matrixTests: matrixStats GSReg: Homo.sapiens org.Hs.eg.db GenomicFeatures AnnotationDbi preseqR: polynom graphics stats spatialLIBD: SingleCellExperiment shiny golem ggplot2 cowplot plotly viridisLite shinyWidgets Polychrome sessioninfo grid grDevices methods AnnotationHub utils png scater DT ExperimentHub RColorBrewer SummarizedExperiment stats graphics S4Vectors IRanges fields benchmarkme SpatialExperiment BiocFileCache jsonlite tibble readbitmap blimaTestingData: DiscriMiner: tightClust: base utils stats epihet: GenomicRanges IRanges S4Vectors ggplot2 foreach Rtsne igraph data.table doParallel EntropyExplorer graphics stats grDevices pheatmap utils qvalue WGCNA ReactomePA RcppDist: Rcpp RcppArmadillo ggtext: ggplot2 grid gridtext rlang scales rgsepd: DESeq2 goseq gplots biomaRt org.Hs.eg.db GO.db SummarizedExperiment hash AnnotationDbi highcharter: htmlwidgets magrittr purrr rlist assertthat zoo dplyr tibble stringr broom xts quantmod tidyr htmltools jsonlite igraph lubridate yaml rlang rjson CeTF: methods circlize ComplexHeatmap clusterProfiler DESeq2 GenomicTools GenomicTools.fileHandler ggnetwork GGally ggplot2 ggpubr ggrepel graphics grid igraph Matrix network Rcpp RCy3 S4Vectors stats SummarizedExperiment utils WebGestaltR RcppArmadillo CellaRepertorium: dplyr tibble stringr Biostrings Rcpp reshape2 methods rlang purrr Matrix S4Vectors BiocGenerics tidyr forcats progress stats utils plotGrouper: ggplot2 dplyr tidyr tibble stringr readr readxl scales stats grid gridExtra egg gtable ggpubr shiny shinythemes colourpicker magrittr Hmisc rlang hms: ellipsis lifecycle methods pkgconfig rlang vctrs ggwordcloud: ggplot2 grid Rcpp scales colorspace png systemPipeR: Rsamtools Biostrings ShortRead methods GenomicRanges GenomicFeatures SummarizedExperiment VariantAnnotation rjson ggplot2 limma edgeR DESeq2 GOstats GO.db annotate pheatmap batchtools yaml stringr assertthat magrittr DOT rsvg IRanges parathyroidSE: SummarizedExperiment HPAStainR: dplyr tidyr utils stats scales stringr tibble shiny data.table uniqtag: survivalROC: mcbiopi: methods seqCAT: GenomicRanges VariantAnnotation dplyr GenomeInfoDb ggplot2 grid IRanges methods rtracklayer rlang scales S4Vectors stats SummarizedExperiment tidyr utils 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 pathifier: R.oo princurve generics: methods arsenal: stats knitr utils RTCGA.RPPA: RTCGA Sconify: tibble dplyr FNN flowCore Rtsne ggplot2 magrittr utils stats readr grDevices: Rhisat2: GenomicFeatures SGSeq GenomicRanges methods utils methylumi: Biobase methods scales reshape2 ggplot2 matrixStats FDb.InfiniumMethylation.hg19 minfi BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges SummarizedExperiment graphics lattice annotate genefilter AnnotationDbi stats4 illuminaio a4Base: a4Preproc a4Core methods graphics grid Biobase annaffy mpm genefilter limma multtest glmnet gplots microRNA: Biostrings GeneGeneInteR: snpStats mvtnorm Rsamtools igraph kernlab FactoMineR IRanges GenomicRanges data.table grDevices graphics stats utils methods GGtools textshaping: systemfonts cpp11 HilbertCurve: grid methods utils HilbertVis png grDevices circlize IRanges GenomicRanges polylabelr FourCSeq: splines LSD DESeq2 ggplot2 Biobase Biostrings GenomicRanges SummarizedExperiment Rsamtools ggbio reshape2 rtracklayer fda GenomicAlignments gtools Matrix methods BiocPkgTools: htmlwidgets BiocFileCache BiocManager biocViews tibble methods rlang tidyselect stringr rvest rex dplyr xml2 rappdirs readr httr htmltools DT tools utils igraph tidyr jsonlite gh RBGL graph magrittr ggfortify: methods ggplot2 dplyr tidyr gridExtra grid scales stringr tibble ExpressionView: caTools bitops methods isa2 eisa GO.db KEGG.db AnnotationDbi flowType: Rcpp BH Biobase graphics grDevices methods flowCore flowMeans sfsmisc rrcov flowClust flowMerge stats EnvStats: MASS ggplot2 nortest vsn: Biobase methods affy limma lattice ggplot2 codetools: Spaniel: Seurat SingleCellExperiment SummarizedExperiment dplyr methods ggplot2 scater shiny jpeg magrittr utils S4Vectors DNABarcodeCompatibility: dplyr tidyr numbers purrr stringr DNABarcodes stats utils methods maanova: Biobase graphics grDevices methods stats utils preciseTAD: S4Vectors IRanges GenomicRanges randomForest ModelMetrics e1071 PRROC pROC caret DMwR utils cluster dbscan doSNOW foreach pbapply stats parallel zebrafishRNASeq: crmn: pcaMethods Biobase methods msgbsR: GenomicRanges methods BSgenome easyRNASeq edgeR GenomicAlignments GenomicFeatures GenomeInfoDb ggbio ggplot2 IRanges parallel plyr Rsamtools R.utils stats SummarizedExperiment S4Vectors utils VERSO: ape parallel Rfast stats MKmisc: stats utils graphics grDevices RColorBrewer robustbase ggplot2 scales limma sigclust: methods fdrtool: graphics grDevices stats ChemoSpecUtils: plyr synapterdata: synapter utils yeastCC: Biobase Mulcom: Biobase graphics grDevices stats methods fields CellBench: SingleCellExperiment magrittr methods stats tibble utils BiocFileCache BiocParallel dplyr rlang glue memoise purrr rappdirs tidyr tidyselect lubridate odseq: msa kebabs mclust bsseq: methods BiocGenerics GenomicRanges SummarizedExperiment IRanges GenomeInfoDb scales stats graphics Biobase locfit gtools data.table S4Vectors R.utils DelayedMatrixStats permute limma DelayedArray Rcpp BiocParallel BSgenome Biostrings utils HDF5Array rhdf5 beachmat ExCluster: Rsubread GenomicRanges rtracklayer matrixStats IRanges stats methods grDevices graphics utils gstat: utils stats graphics methods lattice sp zoo spacetime FNN shinyjqui: shiny htmltools htmlwidgets jsonlite scrime: methods stats utils igvR: GenomicRanges GenomicAlignments BrowserViz methods BiocGenerics httpuv utils MotifDb seqLogo rtracklayer VariantAnnotation RColorBrewer loci2path: pheatmap wordcloud RColorBrewer data.table methods grDevices stats graphics GenomicRanges BiocParallel S4Vectors tRanslatome: methods limma sigPathway anota DESeq edgeR RankProd topGO org.Hs.eg.db GOSemSim Heatplus gplots plotrix Biobase tRNAdbImport: GenomicRanges Modstrings Structstrings tRNA Biostrings BiocGenerics stringr xml2 S4Vectors methods httr IRanges utils gep2pep: repo foreach stats utils GSEABase methods Biobase XML rhdf5 digest iterators sampling: MASS lpSolve NLP: utils epiNEM: BoolNet e1071 gtools stats igraph utils lattice latticeExtra RColorBrewer pcalg minet grDevices graph mnem CNVfilteR: IRanges GenomicRanges SummarizedExperiment pracma regioneR assertthat karyoploteR CopyNumberPlots graphics utils VariantAnnotation Rsamtools GenomeInfoDb Biostrings methods ibh: simpIntLists Clonality: DNAcopy grDevices graphics stats utils GenomicDataCommons: magrittr stats httr xml2 jsonlite utils rlang readr GenomicRanges IRanges dplyr rappdirs SummarizedExperiment S4Vectors tibble maCorrPlot: lattice graphics grDevices stats flowCut: flowCore flowDensity Cairo e1071 grDevices graphics stats methods meshes: AnnotationDbi DOSE enrichplot GOSemSim MeSH.db methods rvcheck utils NMF: methods utils pkgmaker registry rngtools cluster graphics stats stringr digest grid grDevices gridBase colorspace RColorBrewer foreach doParallel ggplot2 reshape2 BiocManager Biobase reactome.db: methods AnnotationDbi HTSeqGenie: gmapR ShortRead VariantAnnotation BiocGenerics S4Vectors IRanges GenomicRanges Rsamtools Biostrings chipseq hwriter Cairo GenomicFeatures BiocParallel parallel tools rtracklayer GenomicAlignments VariantTools GenomeInfoDb SummarizedExperiment methods NMI: ggrepel: ggplot2 grid Rcpp rlang scales StarBioTrek: SpidermiR graphite AnnotationDbi e1071 ROCR MLmetrics grDevices igraph reshape2 ggplot2 ica: gcatest: lfa OPWeight: graphics qvalue MASS tibble stats snifter: basilisk reticulate assertthat ChIPexoQual: GenomicAlignments methods utils GenomeInfoDb stats BiocParallel GenomicRanges ggplot2 data.table Rsamtools IRanges S4Vectors biovizBase broom RColorBrewer dplyr scales viridis hexbin rmarkdown GOFunction: methods Biobase graph Rgraphviz GO.db AnnotationDbi SparseM DBI BSgenome.Hsapiens.UCSC.hg18: BSgenome BSgenome.Hsapiens.UCSC.hg19: BSgenome showtext: sysfonts showtextdb grDevices seqTools: methods utils zlibbioc HDCytoData: ExperimentHub SummarizedExperiment flowCore utils methods missMethyl: IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylationEPICanno.ilm10b4.hg19 AnnotationDbi BiasedUrn Biobase BiocGenerics GenomicRanges GO.db IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICmanifest IRanges limma methods methylumi minfi org.Hs.eg.db ruv S4Vectors statmod stringr SummarizedExperiment groHMM: MASS parallel S4Vectors IRanges GenomeInfoDb GenomicRanges GenomicAlignments rtracklayer pkgdown: callr crayon desc digest downlit fs httr magrittr memoise openssl purrr ragg rematch2 rlang rmarkdown tibble tools whisker withr xml2 yaml HTSCluster: edgeR plotrix capushe grDevices graphics stats clusterSeq: methods BiocParallel baySeq graphics stats utils BiocGenerics rTensor: methods survcomp: survival prodlim ipred SuppDists KernSmooth survivalROC bootstrap grid rmeta stats graphics 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 topicmodels: stats4 methods modeltools slam tm lasso2: TCGAMethylation450k: SpatialExtremes: maps fields InPAS: methods Biobase GenomicRanges GenomicFeatures S4Vectors AnnotationDbi BSgenome cleanUpdTSeq Gviz seqinr preprocessCore IRanges GenomeInfoDb depmixS4 limma BiocParallel MotifDb: methods BiocGenerics S4Vectors IRanges GenomicRanges Biostrings rtracklayer splitstackshape matter: BiocParallel Matrix methods stats biglm BiocGenerics ProtGenerics digest irlba utils ArrayTools: affy Biobase methods graphics grDevices limma stats utils xtable sscu: Biostrings seqinr BiocGenerics ensembldb: BiocGenerics GenomicRanges GenomicFeatures AnnotationFilter methods RSQLite DBI Biobase GenomeInfoDb AnnotationDbi rtracklayer S4Vectors Rsamtools IRanges ProtGenerics Biostrings curl geneXtendeR: rtracklayer GO.db data.table dplyr graphics networkD3 RColorBrewer SnowballC tm utils wordcloud AnnotationDbi BiocStyle org.Rn.eg.db ggsignif: ggplot2 slalom: Rcpp RcppArmadillo BH ggplot2 grid GSEABase methods rsvd SingleCellExperiment SummarizedExperiment stats idr: ids: openssl uuid reshape: plyr BSgenome.Hsapiens.UCSC.hg38: BSgenome isoband: grid utils csaw: GenomicRanges SummarizedExperiment Rcpp Matrix BiocGenerics Rsamtools edgeR limma GenomicFeatures AnnotationDbi methods S4Vectors IRanges GenomeInfoDb stats BiocParallel utils Rhtslib zlibbioc kpeaks: graphics stats utils methods qPLEXdata: qPLEXanalyzer utils knitr MSnbase dplyr cmapR: methods rhdf5 data.table flowCore SummarizedExperiment matrixStats R.methodsS3: utils GeneSelectMMD: Biobase MASS graphics stats limma infinityFlow: flowCore stats grDevices utils graphics pbapply matlab png raster grid uwot gtools Biobase generics parallel methods xgboost FRGEpistasis: MASS fda methods stats utils SeqVarTools: SeqArray grDevices graphics stats methods Biobase BiocGenerics gdsfmt GenomicRanges IRanges S4Vectors GWASExactHW logistf Matrix data.table switchBox: pROC gplots regionReport: BiocStyle derfinder DEFormats DESeq2 GenomeInfoDb GenomicRanges knitr knitrBootstrap methods RefManageR rmarkdown S4Vectors SummarizedExperiment utils etrunct: MeSH.Bsu.168.eg.db: MeSHDbi ggbeeswarm: ggplot2 beeswarm vipor NADfinder: BiocGenerics IRanges GenomicRanges S4Vectors SummarizedExperiment graphics methods baseline signal GenomicAlignments GenomeInfoDb rtracklayer limma trackViewer stats utils Rsamtools metap EmpiricalBrownsMethod ATACseqQC corrplot csaw assertthat: tools Ularcirc: AnnotationHub AnnotationDbi BiocGenerics Biostrings BSgenome data.table DT GenomicFeatures GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 ggrepel gsubfn mirbase.db moments Organism.dplyr S4Vectors shiny shinydashboard shinyFiles shinyjs Sushi yaml tximport: utils stats methods CHETAH: ggplot2 SingleCellExperiment gplots shiny plotly pheatmap bioDist dendextend cowplot corrplot grDevices stats graphics reshape2 S4Vectors SummarizedExperiment ConsensusClusterPlus: Biobase ALL graphics stats utils cluster POMA: Biobase broom caret clisymbols ComplexHeatmap crayon dplyr e1071 ggcorrplot ggplot2 ggraph ggrepel glasso glmnet impute knitr limma magrittr mixOmics MSnbase patchwork plotly qpdf randomForest RankProd reshape2 rmarkdown tibble tidyr vegan svGUI: multiHiCcompare: data.table dplyr HiCcompare edgeR BiocParallel qqman pheatmap methods metap GenomicRanges graphics stats utils pbapply GenomeInfoDbData BLMA GenomeInfoDb maskBAD: gcrma affy transcriptR: methods BiocGenerics caret chipseq e1071 GenomicAlignments GenomicRanges GenomicFeatures GenomeInfoDb ggplot2 graphics grDevices IRanges pROC reshape2 Rsamtools rtracklayer S4Vectors stats utils mRMRe: survival igraph methods PREDAsampledata: methods PREDA Biobase affy annotate reconsi: phyloseq KernSmooth reshape2 ggplot2 stats methods graphics grDevices matrixStats ArrayExpressHTS: sampling Rsamtools snow Biobase BiocGenerics Biostrings DESeq GenomicRanges Hmisc IRanges R2HTML RColorBrewer ShortRead XML biomaRt edgeR grDevices graphics methods rJava stats svMisc utils sendmailR bitops Rhtslib AICcmodavg: methods stats graphics lattice MASS Matrix nlme stats4 survival unmarked VGAM xtable clusterSim: cluster MASS ade4 e1071 rgl R2HTML grDevices graphics stats utils multiscan: Biobase utils DESeq2: S4Vectors IRanges GenomicRanges SummarizedExperiment BiocGenerics Biobase BiocParallel genefilter methods stats4 locfit geneplotter ggplot2 Rcpp RcppArmadillo gprofiler2: jsonlite RCurl ggplot2 plotly tidyr crosstalk grDevices gridExtra grid viridisLite dplyr IsoGeneGUI: tcltk xlsx Rcpp tkrplot multtest relimp geneplotter RColorBrewer Iso IsoGene ORCME ORIClust orQA goric ff Biobase jpeg gridSVG: grDevices graphics utils methods grid jsonlite XML classInt: grDevices stats graphics e1071 class KernSmooth metabomxtr: methods Biobase optimx Formula plyr multtest BiocParallel ggplot2 fastDummies: data.table tibble stringr deconstructSigs: reshape2 BSgenome BSgenome.Hsapiens.UCSC.hg19 GenomeInfoDb grDevices graphics utils hiReadsProcessor: Biostrings GenomicAlignments BiocParallel hiAnnotator sonicLength dplyr BiocGenerics GenomicRanges readxl methods OmaDB: httr plyr utils ape Biostrings GenomicRanges IRanges methods topGO jsonlite pd.hg18.60mer.expr: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors RMTstat: rprojroot: glmSparseNet: Matrix MultiAssayExperiment glmnet SummarizedExperiment STRINGdb biomaRt futile.logger sparsebn sparsebnUtils forcats dplyr readr ggplot2 survminer reshape2 stats stringr rlang parallel methods loose.rock ggimage: ggplot2 ggplotify grid jsonlite magick methods rvcheck scales tibble tools maSigPro: Biobase graphics grDevices venn mclust stats MASS hom.Hs.inp.db: methods AnnotationDbi crul: curl R6 urltools httpcode jsonlite mime tensor: MEIGOR: Rsolnp snowfall CNORode deSolve kSamples: SuppDists methods graphics stats NuPoP: transport: grDevices graphics methods stats Rcpp data.table RcppEigen MBttest: stats gplots gtools graphics base utils grDevices tracktables: IRanges GenomicRanges XVector Rsamtools XML tractor.base stringr RColorBrewer methods GPfit: lhs lattice Rhdf5lib: yeastExpData: graph globaltest: methods survival Biobase AnnotationDbi annotate graphics clusteval: parallel mvtnorm Rcpp rngtools: methods digest utils stats parallel topconfects: methods utils stats assertthat ggplot2 invgamma: survminer: ggplot2 ggpubr grid gridExtra magrittr maxstat methods scales survival stats broom dplyr tidyr survMisc purrr tibble rlang ggtext codelink: BiocGenerics methods Biobase limma annotate AssessORFData: DECIPHER utils GOSemSim: AnnotationDbi GO.db methods utils Rcpp lubridate: methods generics Rcpp openCyto: methods Biobase BiocGenerics gtools flowCore flowViz ncdfFlow flowWorkspace flowStats flowClust MASS clue plyr RBGL graph data.table ks RColorBrewer lattice rrcov R.utils Rcpp pcaMethods: Biobase methods BiocGenerics Rcpp MASS skmeans: slam clue cluster stats utils flowTime: flowCore utils dplyr tibble magrittr plyr rlang timescape: htmlwidgets jsonlite stringr dplyr gtools kmlShape: methods class longitudinalData kml lattice SpeCond: mclust Biobase fields hwriter RColorBrewer methods viridis: viridisLite stats ggplot2 gridExtra assertive.base: methods utils EntropyExplorer: seqCNA: GLAD doSNOW adehabitatLT seqCNA.annot methods EGAD: gplots Biobase GEOquery limma arrayQualityMetrics impute RColorBrewer zoo igraph plyr MASS RCurl methods NTW: mvtnorm stats utils rBayesianOptimization: stats utils data.table magrittr foreach GPfit fmsb: ProteoMM: gdata biomaRt ggplot2 ggrepel gtools stats matrixStats graphics mapplots: fmrs: methods survival stats sessioninfo: cli tools utils withr ChIPSeqSpike: rtracklayer tools stringr Rsamtools GenomicRanges IRanges seqplots ggplot2 LSD corrplot methods stats grDevices graphics utils BiocGenerics S4Vectors WriteXLS: utils TVTB: methods utils stats AnnotationFilter BiocGenerics BiocParallel Biostrings ensembldb ensemblVEP GenomeInfoDb GenomicRanges GGally ggplot2 Gviz limma IRanges reshape2 Rsamtools S4Vectors SummarizedExperiment VariantAnnotation COHCAPanno: RTCGA.mutations: RTCGA illuminaHumanv4.db: methods AnnotationDbi org.Hs.eg.db org.Dr.eg.db: methods AnnotationDbi RcppCCTZ: Rcpp clustifyr: cowplot dplyr entropy fgsea ggplot2 Matrix readr rlang scales stringr tibble tidyr stats methods SingleCellExperiment SummarizedExperiment matrixStats S4Vectors proxy httr waldo: cli diffobj fansi glue methods rematch2 rlang tibble PANR: igraph graphics grDevices MASS methods pvclust stats utils RedeR estimability: stats lpSolveAPI: ACE: Biobase QDNAseq ggplot2 grid stats utils methods grDevices GenomicRanges SNPediaR: RCurl jsonlite future.batchtools: future batchtools utils multiClust: mclust ctc survival cluster dendextend amap graphics grDevices actuar: stats graphics expint ballgown: methods GenomicRanges IRanges S4Vectors RColorBrewer splines sva limma rtracklayer Biobase GenomeInfoDb biotmleData: calibrate: MASS SEPIRA: limma corpcor parallel stats nnet: stats utils roxygen2: brew commonmark desc digest knitr methods pkgload purrr R6 Rcpp rlang stringi stringr utils xml2 doRNG: foreach rngtools stats utils iterators BgeeDB: topGO tidyr data.table curl RCurl digest methods stats utils dplyr RSQLite graph Biobase wpm: utils methods cli Biobase SummarizedExperiment config golem shiny DT ggplot2 dplyr rlang stringr shinydashboard shinyWidgets shinycustomloader RColorBrewer logging TxDb.Dmelanogaster.UCSC.dm6.ensGene: GenomicFeatures AnnotationDbi nnTensor: methods fields rTensor plot3D tagcloud ggplot2 BioSeqClass: scatterplot3d Biostrings ipred e1071 klaR randomForest class tree nnet rpart party foreign Biobase utils stats grDevices dlstats: ggplot2 jsonlite magrittr RColorBrewer scales utils PubScore: ggplot2 igraph ggrepel rentrez progress graphics dplyr utils methods intergraph network sna methylKit: GenomicRanges methods IRanges data.table parallel S4Vectors GenomeInfoDb KernSmooth qvalue emdbook Rsamtools gtools fastseg rtracklayer mclust mgcv Rcpp R.utils limma grDevices graphics stats utils Rhtslib zlibbioc samExploreR: ggplot2 Rsubread RNAseqData.HNRNPC.bam.chr14 edgeR grDevices stats graphics MultiBaC: Matrix ggplot2 MultiAssayExperiment ropls graphics methods SomaticSignatures: VariantAnnotation GenomicRanges NMF S4Vectors IRanges GenomeInfoDb Biostrings ggplot2 ggbio reshape2 pcaMethods Biobase methods proxy lassopv: lars stats POST: stats CompQuadForm Matrix survival Biobase GSEABase VariantFiltering: methods BiocGenerics VariantAnnotation utils stats Biobase S4Vectors IRanges RBGL graph AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicRanges SummarizedExperiment GenomicFeatures Rsamtools BSgenome GenomicScores Gviz shiny shinythemes shinyjs DT shinyTree XVector ssviz: methods Rsamtools Biostrings reshape ggplot2 RColorBrewer stats terra: methods Rcpp raster RNASeqR: ggplot2 pathview edgeR methods Rsamtools tools reticulate ballgown gridExtra rafalib FactoMineR factoextra corrplot PerformanceAnalytics reshape2 DESeq2 systemPipeR systemPipeRdata clusterProfiler org.Hs.eg.db org.Sc.sgd.db stringr pheatmap grDevices graphics stats utils DOSE Biostrings parallel ppiStats: ScISI lattice ppiData Biobase Category graph graphics grDevices methods RColorBrewer stats raster: sp Rcpp methods spelling: commonmark xml2 hunspell knitr combi: ggplot2 nleqslv phyloseq tensor stats limma Matrix BB reshape2 alabama cobs Biobase vegan grDevices graphics methods SummarizedExperiment getDEE2: stats utils SummarizedExperiment htm2txt hexbin: methods lattice grid graphics grDevices stats utils mltools: data.table Matrix methods stats glm2: stats discordant: Biobase stats biwt gtools MASS tools rasterVis: methods raster terra lattice latticeExtra stats utils parallel grid grDevices RColorBrewer hexbin sp zoo viridisLite rmelting: Rdpack rJava ini: regutools: AnnotationDbi AnnotationHub Biostrings DBI GenomicRanges Gviz IRanges RCy3 RSQLite S4Vectors methods stats utils BiocFileCache jquerylib: htmltools PAIRADISE: nloptr SummarizedExperiment S4Vectors stats methods abind BiocParallel DAMEfinder: stats GenomeInfoDb GenomicRanges IRanges S4Vectors readr SummarizedExperiment GenomicAlignments stringr plyr VariantAnnotation parallel ggplot2 Rsamtools BiocGenerics methods limma bumphunter Biostrings reshape2 cowplot utils wesanderson: universalmotif: methods stats utils MASS ggplot2 ggseqlogo yaml IRanges Rcpp Rdpack Biostrings BiocGenerics S4Vectors rlang grid RcppThread shinycssloaders: digest glue grDevices shiny ideal: topGO DESeq2 SummarizedExperiment GenomicRanges IRanges S4Vectors ggplot2 heatmaply plotly pheatmap pcaExplorer IHW gplots UpSetR goseq stringr dplyr limma GOstats GO.db AnnotationDbi shiny shinydashboard shinyBS DT rentrez rintrojs ggrepel knitr rmarkdown shinyAce BiocParallel grDevices base64enc methods mtbls2: MGFM: AnnotationDbi annotate adaptest: methods graphics stats utils calibrate origami SummarizedExperiment S4Vectors tmle bigPint: DelayedArray dplyr GGally ggplot2 graphics grDevices grid gridExtra hexbin Hmisc htmlwidgets methods plotly plyr RColorBrewer reshape shiny shinycssloaders shinydashboard stats stringr SummarizedExperiment tidyr utils maps: graphics utils MGFR: biomaRt annotate EnsDb.Mmusculus.v79: ensembldb TeachingDemos: netDx: ROCR pracma ggplot2 RCy3 glmnet igraph reshape2 parallel stats utils MultiAssayExperiment graphics grDevices methods BiocFileCache GenomicRanges bigmemory doParallel foreach combinat rappdirs GenomeInfoDb S4Vectors IRanges RColorBrewer scater netSmooth clusterExperiment Rtsne httr affxparser: xopen: processx MutationalPatterns: GenomicRanges NMF stats S4Vectors BiocGenerics BSgenome VariantAnnotation dplyr tibble purrr tidyr stringr magrittr ggplot2 pracma IRanges GenomeInfoDb Biostrings ggdendro cowplot ggalluvial brglm: profileModel schex: SingleCellExperiment Seurat ggplot2 shiny hexbin stats methods cluster dplyr entropy ggforce scales grid concaveman reutils: assertthat jsonlite methods RCurl stats XML tibble predictionet: igraph catnet penalized RBGL MASS FDb.UCSC.tRNAs: GenomicFeatures AnnotationDbi MIMOSA: MASS plyr reshape Biobase ggplot2 methods Formula data.table pracma MCMCpack coda modeest testthat Rcpp scales dplyr tidyr rlang RcppArmadillo RLMM: graphics grDevices MASS stats utils GA4GHclient: S4Vectors BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges httr IRanges jsonlite methods VariantAnnotation VaSP: ballgown IRanges GenomicRanges S4Vectors Sushi parallel matrixStats GenomicAlignments GenomeInfoDb Rsamtools cluster stats graphics methods SpatialDecon: logNormReg grDevices stats utils graphics lmtest: stats zoo graphics pasillaBamSubset: dotCall64: org.Ce.eg.db: methods AnnotationDbi emojifont: ggplot2 proto showtext sysfonts utils ExperimentSubset: SummarizedExperiment SingleCellExperiment methods Matrix tools: Rgraphviz: methods utils graph grid stats4 graphics grDevices metaMSdata: DMCFB: SummarizedExperiment methods S4Vectors BiocParallel GenomicRanges IRanges utils stats speedglm MASS data.table splines arm rtracklayer benchmarkme tibble matrixStats fastDummies graphics Maaslin2: robustbase biglm pcaPP edgeR metagenomeSeq lpsymphony pbapply car dplyr vegan chemometrics ggplot2 pheatmap logging data.table lmerTest hash optparse MuMIn grDevices stats utils glmmTMB MASS cplm pscl MetaboSignal: KEGGgraph hpar igraph RCurl KEGGREST EnsDb.Hsapiens.v75 stats graphics utils org.Hs.eg.db biomaRt AnnotationDbi MWASTools mygene topdownrdata: topdownr parallelMap: BBmisc checkmate parallel stats utils scales: farver labeling lifecycle munsell R6 RColorBrewer viridisLite statTarget: randomForest plyr pdist ROC utils grDevices graphics rrcov stats pls impute Rtpca: stats dplyr tidyr Biobase methods ggplot2 pROC fdrtool splines utils tibble randtests: scoreInvHap: Biostrings methods snpStats VariantAnnotation GenomicRanges BiocParallel graphics SummarizedExperiment ReactomePA: AnnotationDbi DOSE enrichplot ggplot2 ggraph reactome.db igraph graphite miRcompData: utils marr: Rcpp SummarizedExperiment utils methods ggplot2 dplyr magrittr rlang S4Vectors RcppAlgos: gmp Rcpp methods RcppThread phateR: Matrix methods stats graphics reticulate ggplot2 memoise periodicDNA: Biostrings GenomicRanges IRanges BSgenome BiocParallel S4Vectors rtracklayer stats GenomeInfoDb magrittr zoo ggplot2 methods parallel cowplot BiocGenerics: methods utils graphics stats parallel manipulateWidget: shiny miniUI htmltools htmlwidgets knitr methods tools base64enc grDevices codetools webshot TOAST: RefFreeEWAS EpiDISH limma nnls stats methods SummarizedExperiment corpcor PAST: stats utils dplyr rlang iterators parallel foreach doParallel qvalue rtracklayer ggplot2 GenomicRanges S4Vectors MLInterfaces: Rcpp methods BiocGenerics Biobase annotate cluster gdata pls sfsmisc MASS rpart genefilter fpc ggvis shiny gbm RColorBrewer hwriter threejs mlbench stats4 tools grDevices graphics stats MBAmethyl: BLMA: ROntoTools GSA PADOG limma graph stats utils parallel Biobase metafor methods nor1mix: stats graphics proxyC: methods Matrix Rcpp RcppParallel RcppArmadillo Harshlight: affy altcdfenvs Biobase stats utils dmrseq: bsseq GenomicRanges nlme ggplot2 S4Vectors RColorBrewer bumphunter DelayedMatrixStats matrixStats BiocParallel outliers methods locfit IRanges grDevices graphics stats utils annotatr AnnotationHub rtracklayer GenomeInfoDb splines GraphPAC: iPAC igraph TSP RMallow condformat: dplyr grDevices gridExtra gtable htmlTable htmltools knitr magrittr openxlsx rmarkdown rlang scales tibble tidyselect Director: htmltools utils grDevices cyclocomp: callr crayon desc remotes withr nleqslv: hgu133plus2probe: AnnotationDbi bladderbatch: Biobase tree: grDevices graphics stats Starr: Ringo affy affxparser pspline MASS zlibbioc 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 farver: FamAgg: methods kinship2 igraph gap Matrix BiocGenerics utils survey emdbook: MASS lattice plyr coda bbmle IgGeneUsage: methods Rcpp SummarizedExperiment StanHeaders rstan reshape2 sqldf: gsubfn proto RSQLite DBI chron lavaan: methods stats4 stats utils graphics MASS mnormt pbivnorm numDeriv sparseDOSSA: stats utils optparse MASS tmvtnorm MCMCpack irr: lpSolve Modstrings: Biostrings methods BiocGenerics GenomicRanges S4Vectors IRanges XVector stringi stringr crayon grDevices tensorA: stats keras: generics reticulate tensorflow tfruns magrittr zeallot methods R6 rlang FlowSorted.CordBloodNorway.450k: minfi pathview: KEGGgraph XML Rgraphviz graph png AnnotationDbi org.Hs.eg.db KEGGREST methods utils plasmodiumanophelescdf: utils AnnotationDbi MEDME: grDevices graphics methods stats utils Biostrings MASS drc lifecycle: glue rlang arrayQuality: graphics grDevices grid gridBase hexbin limma marray methods RColorBrewer stats utils sparseMatrixStats: MatrixGenerics Rcpp Matrix matrixStats methods metaArray: Biobase MergeMaid graphics stats factoextra: ggplot2 abind cluster dendextend FactoMineR ggpubr grid stats reshape2 ggrepel tidyr zinbwave: methods SummarizedExperiment SingleCellExperiment BiocParallel softImpute stats genefilter edgeR Matrix BioMVCClass: methods MVCClass Biobase graph Rgraphviz directPA: grDevices graphics stats plotly calibrate tofsims: methods utils ProtGenerics Rcpp ALS alsace signal KernSmooth graphics grDevices stats RcppArmadillo igraph: methods graphics grDevices magrittr Matrix pkgconfig stats utils nnls: weaver: digest tools utils codetools affydata: affy methods networkD3: htmlwidgets igraph magrittr quantsmooth: quantreg grid KEGG.db: methods AnnotationDbi lumiBarnes: Biobase lumi DEsubs: locfit graph igraph RBGL circlize limma edgeR EBSeq NBPSeq DESeq stats grDevices graphics pheatmap utils ggplot2 Matrix jsonlite tools DESeq2 methods BioMark: pls glmnet MASS st MSGFgui: mzR xlsx shiny mzID MSGFplus shinyFiles tools receptLoss: dplyr ggplot2 magrittr tidyr SummarizedExperiment RandomWalkRestartMH: igraph Matrix dnet methods mAPKL: Biobase multtest clusterSim apcluster limma e1071 AnnotationDbi methods parmigene igraph reactome.db clusterProfiler: AnnotationDbi downloader DOSE dplyr enrichplot GO.db GOSemSim magrittr methods plyr qvalue rlang rvcheck stats tidyr utils compositions: methods utils grDevices stats tensorA robustbase bayesm graphics MASS hmdbQuery: XML S4Vectors methods utils PERFect: sn ggplot2 phyloseq zoo psych stats Matrix fitdistrplus parallel BioCor: BiocParallel Matrix methods GSEABase mathjaxr: agricolae: klaR MASS nlme cluster AlgDesign graphics servr: mime httpuv xfun jsonlite COMPASS: methods Rcpp data.table RColorBrewer scales grid plyr knitr abind clue grDevices utils pdist magrittr reshape2 dplyr tidyr rlang BiocStyle rmarkdown foreach coda GenVisR: methods AnnotationDbi biomaRt BiocGenerics Biostrings DBI FField GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales viridis data.table BSgenome GenomeInfoDb VariantAnnotation phosphonormalizer: plyr stats graphics matrixStats methods tidyHeatmap: methods stats utils dplyr magrittr tidyr rlang purrr tibble ComplexHeatmap viridis circlize RColorBrewer grid grDevices lifecycle ALL: Biobase purrr: magrittr rlang SplicingGraphs: GenomicFeatures GenomicAlignments Rgraphviz methods utils graphics igraph BiocGenerics S4Vectors BiocParallel IRanges GenomeInfoDb GenomicRanges Rsamtools graph kriging: strandCheckR: dplyr magrittr GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools S4Vectors grid BiocGenerics ggplot2 reshape2 stats gridExtra TxDb.Hsapiens.UCSC.hg38.knownGene methods stringr ALS: nnls Iso flowSpy: igraph FlowSOM Rtsne ggplot2 destiny gmodels flowUtils Biobase Matrix flowCore sva matrixStats methods mclust prettydoc RANN Rcpp BiocNeighbors cluster pheatmap scatterpie umap scatterplot3d limma stringr grDevices grid stats msgps: gWidgets2: methods digest biganalytics: stats utils bigmemory foreach biglm Rcpp BH PAA: Rcpp e1071 gplots gtools limma MASS mRMRe randomForest ROCR sva PerfMeas: limma graph RBGL CGHregions: methods Biobase CGHbase Rgin: RcppEigen mboost: methods stats parallel stabs Matrix survival splines lattice nnls quadprog utils graphics grDevices partykit CoverageView: methods Rsamtools rtracklayer S4Vectors IRanges GenomicRanges GenomicAlignments parallel tools rcdklibs: rJava 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 trio: grDevices graphics methods stats survival utils siggenes LogicReg Oncotree: boot Rdisop: Rcpp philentropy: Rcpp dplyr KernSmooth rtracklayer: methods GenomicRanges XML BiocGenerics S4Vectors IRanges XVector GenomeInfoDb Biostrings zlibbioc RCurl Rsamtools GenomicAlignments tools netbenchmark: grndata Rcpp minet GENIE3 c3net PCIT GeneNet tools pracma Matrix corpcor fdrtool harmonicmeanp: FMStable a4Core: Biobase glmnet methods stats ggdendro: MASS ggplot2 vulcan: ChIPpeakAnno TxDb.Hsapiens.UCSC.hg19.knownGene zoo GenomicRanges S4Vectors viper DiffBind locfit wordcloud csaw gplots stats utils caTools graphics DESeq Biobase scatterpie: ggplot2 ggforce rlang rvcheck stats tidyr utils targetscan.Hs.eg.db: methods AnnotationDbi ANF: igraph Biobase survival MASS stats RColorBrewer pwrEWAS: shinyBS foreach doParallel abind truncnorm CpGassoc shiny ggplot2 parallel shinyWidgets BiocManager doSNOW limma genefilter stats grDevices methods utils graphics pwrEWAS.data alevinQC: rmarkdown tools methods ggplot2 GGally dplyr rjson shiny shinydashboard DT stats utils tximport cowplot rlang grndata: celldex: SummarizedExperiment utils ExperimentHub AnnotationHub AnnotationDbi S4Vectors DelayedArray DelayedMatrixStats GenSA: future: digest globals listenv parallel parallelly tools utils ComplexHeatmap: methods grid graphics stats grDevices circlize GetoptLong colorspace clue RColorBrewer GlobalOptions parallel png Cairo digest S4Vectors IRanges matrixStats SIMAT: Rcpp mzR ggplot2 grid reshape2 grDevices stats utils NarrowPeaks: splines BiocGenerics S4Vectors IRanges GenomicRanges GenomeInfoDb fda CSAR ICSNP qpcrNorm: methods Biobase limma affy TPP2D: stats utils dplyr methods ggplot2 tidyr foreach doParallel openxlsx stringr RCurl parallel MASS BiocParallel limma mpmi: KernSmooth mGSZ: Biobase GSA limma MASS ismev FindMyFriends: methods BiocGenerics Biobase tools dplyr IRanges Biostrings S4Vectors kebabs igraph Matrix digest filehash Rcpp ggplot2 gtable grid reshape2 ggdendro BiocParallel utils stats bgmm: mvtnorm car lattice combinat TxDb.Hsapiens.UCSC.hg18.knownGene: GenomicFeatures AnnotationDbi SpikeIn: affy soGGi: BiocGenerics SummarizedExperiment methods reshape2 ggplot2 S4Vectors IRanges GenomeInfoDb GenomicRanges Biostrings Rsamtools GenomicAlignments rtracklayer preprocessCore chipseq BiocParallel R.matlab: methods utils R.methodsS3 R.oo R.utils Mus.musculus: AnnotationDbi methods OrganismDbi GenomicFeatures GO.db org.Mm.eg.db TxDb.Mmusculus.UCSC.mm10.knownGene Rfastp: Rcpp rjson ggplot2 reshape2 Rhtslib zlibbioc TileDBArray: DelayedArray methods Rcpp tiledb S4Vectors contiBAIT: BH Rsamtools data.table grDevices clue cluster gplots BiocGenerics S4Vectors IRanges GenomicRanges Rcpp TSP GenomicFiles gtools rtracklayer BiocParallel DNAcopy colorspace reshape2 ggplot2 methods exomeCopy GenomicAlignments diagram lazyeval: metahdep: methods PFAM.db: methods AnnotationDbi Qtlizer: httr curl GenomicRanges stringi polyester: Biostrings IRanges S4Vectors logspline limma zlibbioc divergence: SummarizedExperiment ARRmData: RefManageR: xml2 jsonlite utils plyr tools httr lubridate stringr methods diffHic: GenomicRanges InteractionSet SummarizedExperiment Rsamtools Rhtslib Biostrings BSgenome rhdf5 edgeR limma csaw locfit methods IRanges S4Vectors GenomeInfoDb BiocGenerics grDevices graphics stats utils Rcpp rtracklayer zlibbioc GeoDE: Matrix MASS pepStat: Biobase IRanges limma fields GenomicRanges ggplot2 plyr tools methods data.table GEOsubmission: affy Biobase utils GSEAlm: Biobase healthyFlowData: flowCore methods GEOmetadb: GEOquery RSQLite RUnit: utils methods graphics webutils: curl jsonlite BioTIP: igraph cluster psych stringr GenomicRanges Hmisc MASS Rsamtools: methods GenomeInfoDb GenomicRanges Biostrings utils BiocGenerics S4Vectors IRanges XVector zlibbioc bitops BiocParallel stats Rhtslib ChemmineOB: methods BiocGenerics zlibbioc Rcpp BH ATACseqQC: BiocGenerics S4Vectors BSgenome Biostrings ChIPpeakAnno IRanges GenomicRanges GenomicAlignments GenomeInfoDb GenomicScores graphics grid limma Rsamtools randomForest rtracklayer stats motifStack preseqR utils KernSmooth edgeR sets: graphics grDevices stats utils GOexpress: grid stats graphics Biobase biomaRt stringr ggplot2 RColorBrewer gplots randomForest RCurl glue: methods a4Preproc: BiocGenerics Biobase PolyPhen.Hsapiens.dbSNP131: VariantAnnotation RSQLite AnnotationDbi org.Xl.eg.db: methods AnnotationDbi freetypeharfbuzz: fontquiver sampSurf: methods sp raster boot lattice latticeExtra rasterVis forcats: ellipsis magrittr rlang tibble TADCompare: dplyr PRIMME cluster Matrix magrittr HiCcompare ggplot2 tidyr ggpubr RColorBrewer reshape2 cowplot genomeIntervals: methods intervals BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors CGHbase: methods Biobase marray LINC: methods stats Rcpp DOSE ggtree gridExtra ape grid png Biobase sva reshape2 utils grDevices org.Hs.eg.db clusterProfiler ggplot2 ReactomePA CAMERA: methods Biobase xcms RBGL graph graphics grDevices stats utils Hmisc igraph PhenStat: SmoothWin methods car nlme nortest MASS msgps logistf knitr tools pingr ggplot2 reshape corrplot graph lme4 graphics grDevices utils stats BAC: pbapply: parallel genotypeeval: VariantAnnotation ggplot2 rtracklayer BiocGenerics GenomicRanges GenomeInfoDb IRanges methods BiocParallel graphics stats mppa: methods stats ndexr: igraph httr jsonlite plyr tidyr martini: igraph Matrix methods Rcpp snpStats S4Vectors stats utils Rgin RcppEigen TxDb.Hsapiens.UCSC.hg19.knownGene: GenomicFeatures AnnotationDbi PathwaySplice: goseq Biobase DOSE reshape2 igraph org.Hs.eg.db org.Mm.eg.db BiocGenerics AnnotationDbi JunctionSeq BiasedUrn GO.db gdata geneLenDataBase grDevices graphics stats utils VennDiagram RColorBrewer ensembldb AnnotationHub S4Vectors dplyr plotly webshot htmlwidgets mgcv gridExtra grid gplots tibble EnrichmentBrowser annotate KEGGREST mirbase.db: methods AnnotationDbi dasper: basilisk BiocFileCache BiocParallel data.table dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges magrittr megadepth methods plyranges readr reticulate S4Vectors stringr SummarizedExperiment tidyr apeglm: emdbook SummarizedExperiment GenomicRanges methods stats utils Rcpp RcppEigen RcppNumerical gpaExample: DBChIP: edgeR DESeq ChIPseeker: AnnotationDbi BiocGenerics boot enrichplot IRanges GenomeInfoDb GenomicRanges GenomicFeatures ggplot2 gplots graphics grDevices gtools methods plotrix dplyr parallel magrittr RColorBrewer rtracklayer S4Vectors stats TxDb.Hsapiens.UCSC.hg19.knownGene utils treemap: colorspace data.table ggplot2 grid gridBase igraph methods RColorBrewer shiny stepNorm: marray methods MASS stats RcppThread: gghalves: ggplot2 grid gtable grDevices R.oo: R.methodsS3 methods utils threejs: igraph htmlwidgets base64enc crosstalk methods stats CONFESS: grDevices utils stats graphics methods changepoint cluster contrast data.table ecp EBImage flexmix flowCore flowClust flowMeans flowMerge flowPeaks foreach ggplot2 grid limma MASS moments outliers parallel plotrix raster readbitmap reshape2 SamSPECTRAL waveslim wavethresh zoo FilterFFPE: foreach doParallel GenomicRanges IRanges Rsamtools parallel S4Vectors SPONGE: Biobase stats ppcor logging foreach doRNG data.table MASS expm gRbase glmnet igraph iterators SeqGSEA: Biobase doParallel DESeq methods biomaRt methyvim: stats cluster methods ggplot2 ggsci gridExtra superheat dplyr gtools tmle future doFuture S4Vectors BiocGenerics BiocParallel SummarizedExperiment GenomeInfoDb bumphunter IRanges limma minfi FoldGO: topGO ggplot2 tidyr stats methods mAPKLData: EasyqpcR: plyr matrixStats plotrix gWidgetsRGtk2 PGA: IRanges GenomicRanges Biostrings data.table rTANDEM S4Vectors Rsamtools GenomicFeatures biomaRt stringr RCurl Nozzle.R1 VariantAnnotation rtracklayer RSQLite ggplot2 AnnotationDbi customProDB pheatmap dplyr processx readr seqinr mpra: methods BiocGenerics SummarizedExperiment limma S4Vectors scales stats graphics statmod IlluminaHumanMethylationEPICanno.ilm10b4.hg19: minfi gtrellis: grid IRanges GenomicRanges circlize GetoptLong grDevices utils BiasedUrn: Logolas: grid SQUAREM LaplacesDemon stats graphics utils ggplot2 gridBase Biostrings chromPlot: stats utils graphics grDevices datasets base biomaRt GenomicRanges pspline: stats graphics BrainSABER: biomaRt SummarizedExperiment data.table lsa methods S4Vectors utils BiocFileCache C50: partykit Cubist MLSeq: caret ggplot2 methods DESeq2 edgeR limma Biobase SummarizedExperiment plyr foreach utils sSeq xtable gridExtra: gtable grid grDevices graphics utils proBAMr: IRanges AnnotationDbi GenomicRanges Biostrings GenomicFeatures rtracklayer biovizBase: methods grDevices stats scales Hmisc RColorBrewer dichromat BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges SummarizedExperiment Biostrings Rsamtools GenomicAlignments GenomicFeatures AnnotationDbi VariantAnnotation ensembldb AnnotationFilter rlang seqPattern: methods Biostrings GenomicRanges IRanges KernSmooth plotrix xps: methods utils pd.huex.1.0.st.v2: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors bigrquery: assertthat bit64 curl DBI gargle glue httr jsonlite methods prettyunits progress Rcpp rlang tibble rapidjsonr TBSignatureProfiler: ASSIGN GSVA SummarizedExperiment S4Vectors methods BiocParallel ComplexHeatmap RColorBrewer ggplot2 reshape2 circlize glmnet ROCit bioDist readr boot DESeq2 caret ggfortify e1071 DT edgeR singscore gdata shiny rslurm: whisker promises: R6 Rcpp later rlang stats magrittr DescTools: base stats graphics grDevices methods MASS utils boot mvtnorm expm Rcpp rstudioapi Exact gld data.table BH biobtreeR: httr httpuv stringi jsonlite methods utils flowWorkspaceData: colorspace: methods graphics grDevices stats ScISI: GO.db RpsiXML annotate apComplex AnnotationDbi methods org.Sc.sgd.db utils prabclus: MASS mclust TxDb.Rnorvegicus.UCSC.rn6.refGene: GenomicFeatures AnnotationDbi TENxPBMCData: SingleCellExperiment HDF5Array AnnotationHub ExperimentHub RcppProgress: targetscan.Mm.eg.db: methods AnnotationDbi mouse4302frmavecs: genlasso: Matrix igraph diffcyt: flowCore FlowSOM SummarizedExperiment S4Vectors limma edgeR lme4 multcomp dplyr tidyr reshape2 magrittr stats methods utils grDevices graphics ComplexHeatmap circlize grid parsedate: rematch2 lmdme: pls stemHypoxia stats methods limma singleCellTK: SummarizedExperiment SingleCellExperiment DelayedArray Biobase ape batchelor BiocGenerics BiocParallel colourpicker colorspace cowplot cluster ComplexHeatmap data.table DelayedMatrixStats DESeq2 dplyr DT ExperimentHub fields ggplot2 ggplotify ggrepel ggtree gridExtra GSVA GSVAdata igraph KernSmooth limma MAST Matrix matrixStats methods msigdbr multtest plotly RColorBrewer ROCR Rtsne S4Vectors scater scMerge scran Seurat shiny shinyFiles shinyWidgets shinyjs shinyBS shinyjqui sva reshape2 AnnotationDbi shinyalert circlize enrichR celda shinycssloaders shinythemes uwot DropletUtils scds reticulate tools withr GSEABase R.utils zinbwave scRNAseq TENxPBMCData yaml rmarkdown magrittr kableExtra scDblFinder BubbleTree: IRanges GenomicRanges plyr dplyr magrittr BiocGenerics BiocStyle Biobase ggplot2 WriteXLS gtools RColorBrewer limma grid gtable gridExtra biovizBase e1071 methods grDevices stats utils corral: ggplot2 ggthemes grDevices gridExtra irlba Matrix methods MultiAssayExperiment pals SingleCellExperiment SummarizedExperiment transport MMAPPR2data: Rsamtools mygene: GenomicFeatures httr jsonlite S4Vectors Hmisc sqldf plyr MeSH.db: MeSHDbi COHCAP: WriteXLS COHCAPanno RColorBrewer gplots Rcpp RcppArmadillo BH HiLDA: ggplot2 R2jags abind cowplot grid forcats stringr GenomicRanges S4Vectors XVector Biostrings GenomicFeatures BSgenome.Hsapiens.UCSC.hg19 BiocGenerics tidyr grDevices stats TxDb.Hsapiens.UCSC.hg19.knownGene utils methods Rcpp PCAN: BiocParallel grDevices stats CompQuadForm: tscR: dplyr gridExtra methods dtw class kmlShape graphics cluster RColorBrewer grDevices knitr rmarkdown prettydoc grid ggplot2 latex2exp stats SummarizedExperiment GenomicRanges IRanges S4Vectors metabolomicsWorkbenchR: data.table httr jsonlite methods MultiAssayExperiment struct SummarizedExperiment utils scmeth: knitr rmarkdown bsseq AnnotationHub GenomicRanges reshape2 stats utils BSgenome DelayedArray annotatr SummarizedExperiment GenomeInfoDb Biostrings DT HDF5Array mclust: stats utils graphics grDevices OSAT: methods stats EpiTxDb.Hs.hg38: AnnotationHub EpiTxDb BSgenome.Drerio.UCSC.danRer7: BSgenome Rmagic: Matrix methods stats reticulate ggplot2 GGBase: methods snpStats limma genefilter Biobase BiocGenerics S4Vectors IRanges Matrix AnnotationDbi digest GenomicRanges SummarizedExperiment yeastNagalakshmi: ABarray: Biobase graphics grDevices methods multtest stats tcltk utils OmicsMarkeR: graphics stats utils plyr data.table caret DiscriMiner e1071 randomForest gbm pamr glmnet caTools foreach permute assertive assertive.base vdiffr: devtools diffobj fontquiver freetypeharfbuzz gdtools glue grDevices htmlwidgets htmltools purrr rlang R6 Rcpp shiny testthat usethis xml2 BH FunciSNP.data: IRanges rtracklayer consensusOV: Biobase GSVA gdata genefu limma matrixStats randomForest stats utils methods TypeInfo: methods evaluate: methods BBCAnalyzer: SummarizedExperiment VariantAnnotation Rsamtools grDevices GenomicRanges IRanges Biostrings copula: stats graphics methods stats4 Matrix lattice colorspace gsl ADGofTest stabledist mvtnorm pcaPP pspline numDeriv GSAR: igraph stats graphics RNAmodR.ML: RNAmodR methods BiocGenerics S4Vectors IRanges GenomicRanges stats ranger slinky: SummarizedExperiment curl dplyr foreach httr stats utils methods readr rhdf5 jsonlite tidyr sparseinv: Matrix methods Rcpp spam lmerTest: lme4 stats methods numDeriv MASS ggplot2 eudysbiome: plyr Rsamtools R.utils Biostrings DelayedArray: methods stats4 Matrix BiocGenerics MatrixGenerics S4Vectors IRanges stats gridtext: grid grDevices markdown rlang Rcpp RCurl png jpeg stringr xml2 pd.genomewidesnp.5: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors pd.genomewidesnp.6: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors BHC: rBiopaxParser: data.table XML plgem: utils Biobase MASS methods assertive.datetimes: assertive.base assertive.types EBSeqHMM: EBSeq GSCA: shiny sp gplots ggplot2 reshape2 RColorBrewer rhdf5 graphics xts: zoo methods RPostgreSQL: methods DBI IlluminaHumanMethylation450kmanifest: minfi fmcsR: ChemmineR methods RUnit BiocGenerics parallel GeneExpressionSignature: Biobase PGSEA arrayMvout: tools methods utils parody Biobase affy lumi simpleaffy mdqc affyContam drosophila2probe: AnnotationDbi xmapbridge: methods EmpiricalBrownsMethod: HelloRangesData: RhpcBLASctl: seqsetvis: ggplot2 data.table eulerr GenomeInfoDb GenomicAlignments GenomicRanges grDevices grid IRanges limma methods pbapply pbmcapply png RColorBrewer Rsamtools rtracklayer S4Vectors stats biocthis: BiocManager fs glue rlang styler usethis PMA: flowClean: flowCore bit changepoint sfsmisc ChIC: spp ChIC.data caTools methods GenomicRanges IRanges parallel progress caret grDevices stats utils graphics S4Vectors BiocGenerics SIMLR: parallel Matrix stats methods Rcpp pracma RcppAnnoy RSpectra GRridge: penalized Iso survival methods graph stats glmnet mvtnorm jackstraw: corpcor cluster methods ClusterR qvalue lfa stats irlba rsvd maftools: data.table RColorBrewer methods grDevices survival listenv: tidytext: rlang tibble dplyr stringr hunspell generics lifecycle Matrix tokenizers janeaustenr purrr methods vctrs eulerr: GenSA graphics grDevices grid polyclip polylabelr Rcpp stats utils RcppArmadillo iPAC: gdata scatterplot3d Biostrings multtest showtextdb: sysfonts utils ensemblVEP: methods BiocGenerics GenomicRanges VariantAnnotation S4Vectors Biostrings SummarizedExperiment GenomeInfoDb stats MethPed: Biobase randomForest grDevices graphics stats optimalFlow: dplyr optimalFlowData rlang transport parallel Rfast robustbase dbscan randomForest foreach graphics doParallel stats flowMeans rgl ellipse hyperdraw: methods grid graph hypergraph Rgraphviz stats4 ellipse: graphics stats epigenomix: methods Biobase S4Vectors IRanges GenomicRanges SummarizedExperiment BiocGenerics MCMCpack Rsamtools parallel GenomeInfoDb beadarray ffpeExampleData: lumi rmarkdown: tools utils knitr yaml htmltools evaluate jsonlite tinytex xfun methods stringr mnormt: tmvnsim glmmTMB: methods TMB lme4 Matrix nlme RcppEigen BiocNeighbors: Rcpp S4Vectors BiocParallel stats methods Matrix RcppHNSW baySeq: methods GenomicRanges abind parallel edgeR upsetjs: htmlwidgets magrittr europepmc: httr jsonlite plyr dplyr progress urltools purrr xml2 tibble tidyr rlang bamsignals: methods BiocGenerics Rcpp IRanges GenomicRanges zlibbioc Rhtslib hgu95a.db: methods AnnotationDbi org.Hs.eg.db MOGAMUN: stats utils RCy3 stringr graphics grDevices RUnit BiocParallel igraph supraHex: hexbin ape MASS grDevices graphics stats readr tibble tidyr dplyr stringr purrr magrittr igraph methods netresponse: Rgraphviz methods minet mclust reshape2 dmt ggplot2 graph igraph parallel plyr qvalue RColorBrewer qqman: calibrate spikeLI: graphics grDevices stats utils annotate: AnnotationDbi XML Biobase DBI xtable graphics utils stats methods BiocGenerics httr BiocWorkflowTools: BiocStyle bookdown git2r httr knitr rmarkdown rstudioapi stringr tools utils usethis shinytest: assertthat callr crayon debugme digest htmlwidgets httpuv httr jsonlite parsedate pingr R6 rematch rlang rstudioapi shiny testthat utils webdriver withr WGCNA: dynamicTreeCut fastcluster stats grDevices utils matrixStats Hmisc impute splines foreach doParallel preprocessCore survival parallel GO.db AnnotationDbi Rcpp ropls: Biobase graphics grDevices methods MultiDataSet stats VGAM: methods stats stats4 splines ggcorrplot: ggplot2 reshape2 stats FISHalyseR: EBImage abind mCSEAdata: transite: BiocGenerics Biostrings dplyr GenomicRanges ggplot2 ggseqlogo grDevices gridExtra methods parallel Rcpp scales stats TFMPvalue utils meshr: methods stats utils fdrtool MeSH.db MeSH.AOR.db MeSH.PCR.db MeSHDbi MeSH.Hsa.eg.db MeSH.Aca.eg.db MeSH.Bsu.168.eg.db MeSH.Syn.eg.db cummeRbund org.Hs.eg.db Category S4Vectors BiocGenerics RSQLite BiocIO: BiocGenerics GenomicRanges RCurl S4Vectors methods tools GeneticsDesign: gmodels graphics gtools mvtnorm stats pdftools: Rcpp qpdf shinycustomloader: glue shiny annotatr: AnnotationDbi AnnotationHub dplyr GenomicFeatures GenomicRanges GenomeInfoDb ggplot2 IRanges methods readr regioneR reshape2 rtracklayer S4Vectors stats utils BANDITS: Rcpp doRNG MASS data.table R.utils doParallel parallel foreach methods stats graphics ggplot2 DRIMSeq BiocParallel RcppArmadillo proftools: summarytools: base64enc checkmate dplyr grDevices htmltools lubridate magick matrixStats methods pander pryr rapportools stats tcltk tibble tidyr utils curatedTCGAData: MultiAssayExperiment AnnotationHub ExperimentHub HDF5Array methods S4Vectors stats SummarizedExperiment utils iC10: pamr impute iC10TrainingData reportr: ore cpp11: SLGI: ScISI lattice AnnotationDbi Biobase GO.db graphics methods stats BiocGenerics omicplotR: ALDEx2 compositions DT grDevices knitr jsonlite matrixStats rmarkdown shiny stats vegan zCompositions BMA: survival leaps robustbase inline rrcov methods XCIR: methods stats utils data.table IRanges VariantAnnotation seqminer ggplot2 biomaRt readxl S4Vectors rstatix: stats utils tidyr purrr broom rlang tibble dplyr magrittr corrplot tidyselect car generics kernlab: methods stats grDevices graphics yamss: methods BiocGenerics SummarizedExperiment IRanges stats S4Vectors EBImage Matrix mzR data.table grDevices limma SNAGEEdata: metaCCA: ggstance: ggplot2 plyr rlang withr pRolocdata: MSnbase Biobase utils MCMCprecision: Rcpp parallel utils stats Matrix combinat RcppArmadillo RcppProgress RcppEigen regsplice: glmnet SummarizedExperiment S4Vectors limma edgeR stats pbapply utils methods ggformula: ggplot2 ggstance scales ggridges mosaicCore rlang magrittr tibble stringr ggforce grid labelled deco: AnnotationDbi BiocParallel SummarizedExperiment limma stats methods ggplot2 foreign graphics BiocStyle Biobase cluster gplots RColorBrewer locfit made4 ade4 sfsmisc scatterplot3d gdata grDevices utils reshape2 gridExtra ROCpAI: boot SummarizedExperiment fission knitr methods MetaCyto: flowCore tidyr fastcluster ggplot2 metafor cluster FlowSOM grDevices graphics stats utils rmeta: grid stats graphics repmis: data.table digest httr plyr R.cache shinyBS: shiny htmltools