EGSEAdata: benchmarkme: benchmarkmeData compiler doParallel dplyr foreach graphics httr Matrix methods parallel stringr tibble utils cellranger: rematch tibble GOSemSim: AnnotationDbi DBI digest GO.db methods rlang R.utils stats utils yulab.utils Rcpp datasets: httr2: cli curl glue lifecycle magrittr openssl R6 rappdirs rlang vctrs withr seqpac: Biostrings foreach GenomicRanges Rbowtie ShortRead tibble BiocParallel cowplot data.table digest doParallel dplyr factoextra FactoMineR ggplot2 IRanges parallel reshape2 rtracklayer stringr stats methods S4Vectors readr remotes: methods stats tools utils rematch2: tibble IRanges: methods utils stats BiocGenerics S4Vectors stats4 GEOquery: methods Biobase readr xml2 dplyr data.table tidyr magrittr limma curl rentrez R.utils stringr SummarizedExperiment S4Vectors rvest httr2 httpuv: later promises R6 Rcpp utils GenomicFeatures: BiocGenerics S4Vectors IRanges Seqinfo GenomicRanges AnnotationDbi methods utils stats DBI XVector Biostrings rtracklayer mgcv: nlme methods stats graphics Matrix splines utils ape: nlme lattice graphics methods stats utils parallel Rcpp digest tidyr: cli dplyr glue lifecycle magrittr purrr rlang stringr tibble tidyselect utils vctrs cpp11 regioneR: GenomicRanges memoise IRanges BSgenome Biostrings rtracklayer parallel graphics stats utils methods Seqinfo GenomeInfoDb S4Vectors tools dbplyr: blob cli DBI dplyr glue lifecycle magrittr methods pillar purrr R6 rlang tibble tidyr tidyselect utils vctrs withr splitstackshape: data.table PoiClaClu: ragg: systemfonts textshaping gargle: cli fs glue httr jsonlite lifecycle openssl rappdirs rlang stats utils withr ggthemes: ggplot2 graphics grid lifecycle methods purrr scales stringr tibble V8: Rcpp jsonlite curl utils GenomeInfoDb: methods BiocGenerics S4Vectors IRanges Seqinfo stats utils UCSC.utils flowWorkspace: Biobase BiocGenerics cytolib XML ggplot2 graph graphics grDevices methods stats stats4 utils RBGL tools Rgraphviz data.table dplyr scales matrixStats RProtoBufLib flowCore ncdfFlow DelayedArray S4Vectors cpp11 BH Rhdf5lib dtplyr: cli data.table dplyr glue lifecycle rlang tibble tidyselect vctrs RCurl: methods bitops highr: xfun tidytree: ape dplyr lazyeval magrittr methods rlang tibble tidyr tidyselect yulab.utils pillar cli bumphunter: S4Vectors IRanges Seqinfo GenomicRanges foreach iterators methods parallel locfit matrixStats limma doRNG BiocGenerics utils GenomicFeatures AnnotationDbi stats highthroughputassays: flowCore flowStats flowWorkspace parallelly: parallel tools utils brio: TCGAWorkflow: AnnotationHub knitr ELMER biomaRt BSgenome.Hsapiens.UCSC.hg19 circlize c3net ChIPseeker ComplexHeatmap ggpubr clusterProfiler downloader GenomicRanges GenomeInfoDb ggplot2 ggthemes graphics minet motifStack pathview pbapply parallel rGADEM pander maftools RTCGAToolbox stringr SummarizedExperiment dplyr plyr matlab MultiAssayExperiment TCGAbiolinks TCGAWorkflowData DT gt FlowSorted.Blood.450k: minfi RcppTOML: Rcpp tseries: graphics stats utils quadprog zoo quantmod jsonlite diffcyt: flowCore FlowSOM SummarizedExperiment S4Vectors limma edgeR lme4 multcomp dplyr tidyr reshape2 magrittr stats methods utils grDevices graphics ComplexHeatmap circlize grid siggenes: Biobase multtest splines methods stats4 grDevices graphics stats scrime ChIPpeakAnno: methods IRanges GenomicRanges S4Vectors AnnotationDbi BiocGenerics Biostrings pwalign DBI dplyr GenomeInfoDb GenomicAlignments GenomicFeatures RBGL Rsamtools SummarizedExperiment VennDiagram biomaRt ggplot2 grDevices graph graphics grid InteractionSet KEGGREST matrixStats multtest regioneR rtracklayer stats utils universalmotif stringr tibble tidyr data.table scales ensembldb txdbmaker: BiocGenerics S4Vectors Seqinfo GenomicRanges GenomicFeatures methods utils stats tools httr rjson DBI RSQLite IRanges UCSC.utils GenomeInfoDb AnnotationDbi Biobase BiocIO rtracklayer biomaRt flowStats: BiocGenerics MASS flowCore flowWorkspace ncdfFlow flowViz fda Biobase methods grDevices graphics stats cluster utils KernSmooth lattice ks RColorBrewer rrcov corpcor mnormt clue backports: tidyverse: broom conflicted cli dbplyr dplyr dtplyr forcats ggplot2 googledrive googlesheets4 haven hms httr jsonlite lubridate magrittr modelr pillar purrr ragg readr readxl reprex rlang rstudioapi rvest stringr tibble tidyr xml2 BSgenome.Mmusculus.UCSC.mm9: BSgenome SingleCellExperiment: SummarizedExperiment methods utils stats S4Vectors BiocGenerics GenomicRanges DelayedArray csaw: GenomicRanges SummarizedExperiment Rcpp Matrix BiocGenerics Rsamtools edgeR limma methods S4Vectors IRanges Seqinfo stats BiocParallel metapod utils Rhtslib enrichplot: aplot DOSE ggfun ggnewscale ggplot2 ggrepel ggtangle graphics grid igraph methods plyr purrr RColorBrewer reshape2 rlang stats tidydr utils scatterpie GOSemSim ggtree yulab.utils RcppEigen: Rcpp stats utils circlize: graphics GlobalOptions shape grDevices utils stats colorspace methods grid bluster: stats methods utils cluster Matrix Rcpp igraph S4Vectors BiocParallel BiocNeighbors assorthead corrplot: setRNG: stats ash: ComplexHeatmap: methods grid graphics stats grDevices circlize GetoptLong colorspace clue RColorBrewer GlobalOptions png digest IRanges matrixStats foreach doParallel codetools bigassertr: pcaPP: mvtnorm methods generics: methods ggfun: cli dplyr ggplot2 grid rlang scales utils yulab.utils methylationArrayAnalysis: knitr rmarkdown BiocStyle limma minfi IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylation450kmanifest RColorBrewer missMethyl matrixStats minfiData Gviz DMRcate stringr FlowSorted.Blood.450k tidydr: cluster ggfun ggplot2 grid rlang stats utils TH.data: survival MASS derfinderHelper: IRanges Matrix methods S4Vectors juicyjuice: V8 prettyunits: flowViz: flowCore lattice stats4 Biobase graphics grDevices grid KernSmooth latticeExtra MASS methods RColorBrewer stats utils hexbin IDPmisc boot: graphics stats emmeans: estimability graphics methods mvtnorm numDeriv rlang stats utils rpart: graphics stats grDevices deldir: graphics grDevices SummarizedExperiment: methods MatrixGenerics GenomicRanges Biobase utils stats tools Matrix BiocGenerics S4Vectors IRanges Seqinfo S4Arrays DelayedArray gridExtra: gtable grid grDevices graphics utils csawUsersGuide: conflicted: cli memoise rlang zoo: stats utils graphics grDevices lattice scrime: methods stats utils ScaledMatrix: methods Matrix S4Vectors DelayedArray biovizBase: methods grDevices stats scales Hmisc RColorBrewer dichromat BiocGenerics S4Vectors IRanges Seqinfo GenomeInfoDb GenomicRanges SummarizedExperiment Biostrings Rsamtools GenomicAlignments GenomicFeatures AnnotationDbi VariantAnnotation ensembldb AnnotationFilter rlang forcats: cli glue lifecycle magrittr rlang tibble splines: graphics stats ELMER.data: GenomicRanges Cairo: grDevices graphics miniUI: shiny htmltools utils org.Rn.eg.db: methods AnnotationDbi profvis: htmlwidgets rlang vctrs macrophage: hugene10sttranscriptcluster.db: methods AnnotationDbi org.Hs.eg.db pkgbuild: callr cli desc processx R6 crayon: grDevices methods utils pkgconfig: utils methods: utils stats edgeR: limma methods graphics stats utils locfit ellipsis: rlang withr: graphics grDevices googlesheets4: cellranger cli curl gargle glue googledrive httr ids lifecycle magrittr methods purrr rematch2 rlang tibble utils vctrs withr RaggedExperiment: GenomicRanges BiocBaseUtils BiocGenerics Seqinfo IRanges Matrix MatrixGenerics methods S4Vectors stats SummarizedExperiment utils R2HTML: stats graphics utils grDevices methods rmarkdown: bslib evaluate fontawesome htmltools jquerylib jsonlite knitr methods tinytex tools utils xfun yaml lambda.r: formatR textshaping: lifecycle stats stringi systemfonts utils cpp11 ExperimentHub: methods BiocGenerics AnnotationHub BiocFileCache utils S4Vectors BiocManager rappdirs oligoClasses: BiocGenerics Biobase methods graphics IRanges GenomicRanges SummarizedExperiment Biostrings affyio foreach BiocManager utils S4Vectors RSQLite DBI ff DirichletMultinomial: S4Vectors IRanges stats4 methods BiocGenerics Biostrings: BiocGenerics S4Vectors IRanges XVector Seqinfo methods utils grDevices stats crayon tinytex: xfun ArrayExpress: Biobase oligo limma httr utils jsonlite rlang tools methods xfun: grDevices stats tools GenomicDataCommons: stats httr xml2 jsonlite utils rlang readr GenomicRanges IRanges dplyr rappdirs tibble tidyr beachmat: methods DelayedArray SparseArray BiocGenerics Matrix Rcpp assorthead nanotubes: dplyr: cli generics glue lifecycle magrittr methods pillar R6 rlang tibble tidyselect utils vctrs dcanr: igraph foreach plyr stringr reshape2 methods Matrix graphics stats RColorBrewer circlize doRNG EDASeq: Biobase ShortRead methods graphics BiocGenerics IRanges aroma.light Rsamtools biomaRt Biostrings AnnotationDbi GenomicFeatures GenomicRanges BiocManager yulab.utils: cli digest fs methods rappdirs rlang tools utils sass: fs rlang htmltools R6 rappdirs gmp: methods ucminf: pan: BeadDataPackR: stats utils FactoMineR: car cluster DT ellipse emmeans flashClust graphics grDevices lattice leaps MASS multcompView scatterplot3d stats utils ggplot2 ggrepel drc: MASS stats car gtools multcomp plotrix scales xtable: stats utils RColorBrewer: topGO: methods BiocGenerics graph Biobase GO.db AnnotationDbi SparseM lattice matrixStats DBI Hmisc: methods ggplot2 cluster rpart nnet foreign gtable grid gridExtra data.table htmlTable viridisLite htmltools base64enc colorspace rmarkdown knitr Formula scatterplot3d: grDevices graphics stats DMRcate: AnnotationHub ExperimentHub bsseq Seqinfo limma edgeR minfi missMethyl GenomicRanges plyr Gviz IRanges stats utils S4Vectors methods graphics SummarizedExperiment biomaRt grDevices interp: Rcpp deldir RcppEigen AnnotationHub: BiocGenerics BiocFileCache utils methods grDevices RSQLite BiocManager BiocVersion curl rappdirs AnnotationDbi S4Vectors httr2 yaml dplyr BiocBaseUtils GetoptLong: rjson GlobalOptions methods crayon openxlsx: grDevices methods Rcpp stats stringi utils zip maftools: data.table grDevices methods RColorBrewer Rhtslib survival DNAcopy pheatmap cowplot: ggplot2 grid gtable grDevices methods rlang scales grid: grDevices utils rnaseqDTU: DRIMSeq DEXSeq stageR DESeq2 edgeR rafalib devtools doParallel: foreach iterators parallel utils vctrs: cli glue lifecycle rlang bbmle: stats4 stats numDeriv lattice MASS methods bdsmatrix Matrix mvtnorm curl: scuttle: SingleCellExperiment methods utils stats Matrix Rcpp BiocGenerics S4Vectors BiocParallel GenomicRanges SummarizedExperiment S4Arrays MatrixGenerics SparseArray DelayedArray beachmat ROCR: methods graphics grDevices gplots stats sequencing: GenomicRanges GenomicAlignments Biostrings Rsamtools ShortRead BiocParallel rtracklayer VariantAnnotation AnnotationHub BSgenome.Hsapiens.UCSC.hg19 RNAseqData.HNRNPC.bam.chr14 desc: cli R6 utils googledrive: cli gargle glue httr jsonlite lifecycle magrittr pillar purrr rlang tibble utils uuid vctrs withr CAGEfightR: GenomicRanges rtracklayer SummarizedExperiment pryr assertthat methods Matrix BiocGenerics S4Vectors IRanges Seqinfo GenomicFeatures GenomicAlignments BiocParallel GenomicFiles Gviz InteractionSet GenomicInteractions sessioninfo: cli tools utils MatrixModels: stats methods Matrix TeachingDemos: spam: dotCall64 grid methods Rcpp globaltest: methods survival Biobase AnnotationDbi annotate graphics RcppThread: plogr: mathjaxr: EnvStats: MASS ggplot2 nortest rprojroot: fontquiver: fontBitstreamVera fontLiberation BSgenome.Hsapiens.UCSC.hg19: BSgenome beadarray: BiocGenerics Biobase hexbin BeadDataPackR limma AnnotationDbi stats4 reshape2 GenomicRanges IRanges illuminaio methods ggplot2 pkgdown: bslib callr cli desc downlit fontawesome fs httr2 jsonlite lifecycle openssl purrr ragg rlang rmarkdown tibble whisker withr xml2 yaml broom: backports cli dplyr generics glue lifecycle purrr rlang stringr tibble tidyr R.oo: R.methodsS3 methods utils KEGGdzPathwaysGEO: Biobase BiocGenerics limma: grDevices graphics stats utils methods statmod bit64: bit graphics methods stats utils pkgload: cli desc fs glue lifecycle methods pkgbuild processx rlang rprojroot utils apeglm: emdbook SummarizedExperiment GenomicRanges methods stats utils Rcpp RcppEigen RcppNumerical Gviz: methods S4Vectors IRanges GenomicRanges grid XVector rtracklayer lattice RColorBrewer biomaRt AnnotationDbi Biobase GenomicFeatures ensembldb BSgenome Biostrings biovizBase Rsamtools latticeExtra matrixStats GenomicAlignments Seqinfo GenomeInfoDb BiocGenerics digest graphics grDevices stats utils fgsea: Rcpp data.table BiocParallel stats ggplot2 cowplot grid fastmatch Matrix scales utils BH locfit: lattice graphlayouts: igraph Rcpp RcppArmadillo regionReport: BiocStyle derfinder DEFormats DESeq2 Seqinfo GenomeInfoDb GenomicRanges knitr knitrBootstrap methods RefManageR rmarkdown S4Vectors SummarizedExperiment utils rhdf5: methods Rhdf5lib rhdf5filters motifmatchr: Matrix Rcpp methods TFBSTools Biostrings BSgenome S4Vectors SummarizedExperiment GenomicRanges IRanges Rsamtools Seqinfo RcppArmadillo callr: processx R6 utils quantreg: stats SparseM methods graphics Matrix MatrixModels survival MASS tibble: cli lifecycle magrittr methods pillar pkgconfig rlang utils vctrs DRIMSeq: utils stats MASS GenomicRanges IRanges S4Vectors BiocGenerics methods BiocParallel limma edgeR ggplot2 reshape2 promises: fastmap later lifecycle magrittr otel R6 rlang hgfocuscdf: utils AnnotationDbi ggupset: ggplot2 gtable grid tibble rlang scales graph: methods BiocGenerics stats stats4 utils mclust: stats utils graphics grDevices bit: cytolib: RProtoBufLib BH Rhdf5lib graphics: grDevices nortest: stats aplot: ggfun ggplot2 ggplotify patchwork magrittr methods utils yulab.utils pillar PADOG: KEGGdzPathwaysGEO methods Biobase limma AnnotationDbi GSA foreach doRNG hgu133plus2.db hgu133a.db KEGGREST nlme rhdf5filters: Rhdf5lib pbkrtest: lme4 broom dplyr MASS methods numDeriv Matrix doBy cluster: graphics grDevices stats utils glue: methods gdtools: fontquiver htmltools Rcpp systemfonts tools openssl: askpass lubridate: methods generics timechange estimability: stats iterators: utils bsseq: methods BiocGenerics GenomicRanges SummarizedExperiment IRanges Seqinfo scales stats parallel tools graphics Biobase locfit gtools data.table S4Vectors R.utils DelayedMatrixStats permute limma DelayedArray Rcpp BiocParallel BSgenome Biostrings utils HDF5Array rhdf5 beachmat assorthead assertthat: tools gginnards: ggplot2 utils methods rlang stringr magrittr tibble robustbase: stats graphics utils methods DEoptimR egg: gridExtra ggplot2 gtable grid grDevices utils ggsignif: ggplot2 tidyselect: cli glue lifecycle rlang vctrs withr mvtnorm: stats quadprog: sourcetools: seriation: ca cluster colorspace foreach gclus grDevices grid MASS qap registry stats TSP vegan crosstalk: htmltools jsonlite lazyeval R6 AnnotationDbi: methods stats4 BiocGenerics Biobase IRanges DBI RSQLite S4Vectors stats KEGGREST Mus.musculus: AnnotationDbi methods OrganismDbi GenomicFeatures GO.db org.Mm.eg.db TxDb.Mmusculus.UCSC.mm10.knownGene ggraph: ggplot2 dplyr ggforce grid igraph scales MASS ggrepel utils stats viridis rlang tidygraph graphlayouts withr cli vctrs lifecycle memoise cpp11 foreign: methods utils stats rnaseqGene: BiocStyle airway tximeta magrittr DESeq2 apeglm vsn dplyr ggplot2 hexbin pheatmap RColorBrewer PoiClaClu glmpca ggbeeswarm genefilter AnnotationDbi org.Hs.eg.db Gviz sva RUVSeq fission ggbeeswarm: ggplot2 beeswarm lifecycle vipor cli KEGGgraph: methods XML graph utils RCurl Rgraphviz affyio: methods infotheo: fontBitstreamVera: MatrixGenerics: matrixStats methods recount: SummarizedExperiment BiocParallel derfinder downloader GEOquery GenomeInfoDb GenomicRanges IRanges methods RCurl rentrez rtracklayer S4Vectors stats utils RNAseq123: Glimma limma edgeR gplots RColorBrewer Mus.musculus R.utils TeachingDemos statmod BiocWorkflowTools OrganismDbi: BiocGenerics AnnotationDbi Seqinfo GenomicFeatures methods utils stats DBI BiocManager Biobase graph RBGL S4Vectors IRanges GenomicRanges rstatix: stats utils tidyr purrr broom rlang tibble dplyr magrittr corrplot tidyselect car generics TCGAbiolinksGUI.data: FlowSOM: igraph stats utils colorRamps ConsensusClusterPlus dplyr flowCore ggforce ggnewscale ggplot2 ggpubr grDevices magrittr methods rlang Rtsne tidyr BiocGenerics XML SparseArray: methods Matrix BiocGenerics MatrixGenerics S4Vectors S4Arrays utils stats matrixStats IRanges XVector h5mread: methods rhdf5 BiocGenerics SparseArray stats tools rhdf5filters S4Vectors IRanges S4Arrays Rhdf5lib GO.db: methods AnnotationDbi MASS: grDevices graphics stats utils methods clipr: utils seqLogo: methods grid stats4 grDevices modelr: broom magrittr purrr rlang tibble tidyr tidyselect vctrs Rbowtie: utils lme4: Matrix methods stats graphics grid splines utils parallel MASS lattice boot nlme minqa nloptr reformulas rlang Rdpack Rcpp RcppEigen RSpectra: Matrix Rcpp RcppEigen git2r: graphics utils RcppML: Rcpp Matrix methods stats RcppEigen reshape2: plyr Rcpp stringr codetools: liftOver: gwascat GenomeInfoDb GenomicRanges rtracklayer Homo.sapiens BiocGenerics TxDb.Scerevisiae.UCSC.sacCer3.sgdGene: GenomicFeatures AnnotationDbi bibtex: backports utils rbibutils: utils tools patchwork: ggplot2 gtable grid stats grDevices utils graphics rlang cli farver utf8: PerformanceAnalytics: xts methods quadprog zoo sitmo: Rcpp ruv: stats ggplot2 scales gridExtra ggseqlogo: ggplot2 ellipse: graphics stats ggbio: methods BiocGenerics ggplot2 grid grDevices graphics stats utils gridExtra scales reshape2 gtable Hmisc biovizBase Biobase S4Vectors IRanges Seqinfo GenomeInfoDb GenomicRanges SummarizedExperiment Biostrings Rsamtools GenomicAlignments BSgenome VariantAnnotation rtracklayer GenomicFeatures OrganismDbi ensembldb AnnotationDbi AnnotationFilter rlang htmltools: base64enc digest fastmap grDevices rlang utils parallel: tools compiler irlba: Matrix stats methods BP4RNAseq: dplyr fastqcr stringr tidyr stats utils magrittr reticulate DBI: methods pheatmap: grid RColorBrewer scales gtable stats grDevices graphics NOISeq: methods Biobase splines Matrix BiasedUrn: MKinfer: stats rlang MKdescr boot arrangements nlme ggplot2 exactRankTests miceadds lobstr: crayon methods prettyunits rlang cpp11 WGCNA: dynamicTreeCut fastcluster stats grDevices utils matrixStats Hmisc impute splines foreach doParallel preprocessCore survival parallel GO.db AnnotationDbi Rcpp readxl: cellranger tibble utils cpp11 progress multcomp: stats graphics mvtnorm survival TH.data sandwich codetools FNN: GenomicAlignments: methods BiocGenerics S4Vectors IRanges Seqinfo GenomicRanges SummarizedExperiment Biostrings Rsamtools utils stats BiocParallel cigarillo RNAseqData.HNRNPC.bam.chr14: TxDb.Mmusculus.UCSC.mm9.knownGene: GenomicFeatures AnnotationDbi fastcluster: scran: SingleCellExperiment scuttle SummarizedExperiment S4Vectors BiocGenerics BiocParallel Rcpp stats methods utils Matrix edgeR limma igraph statmod MatrixGenerics S4Arrays DelayedArray BiocSingular bluster metapod dqrng beachmat BH TFBSTools: Biobase Biostrings pwalign BiocGenerics BiocParallel BSgenome caTools DirichletMultinomial Seqinfo GenomicRanges gtools grid IRanges methods DBI RSQLite rtracklayer seqLogo S4Vectors TFMPvalue XML XVector parallel processx: ps R6 utils mitools: DBI methods stats fastmap: colorspace: methods graphics grDevices stats ca: heatmaply: plotly viridis ggplot2 dendextend magrittr reshape2 scales seriation utils stats grDevices methods colorspace RColorBrewer htmlwidgets webshot assertthat egg xml2: cli methods rlang rappdirs: UCSC.utils: methods stats httr jsonlite S4Vectors clusterProfiler: AnnotationDbi DOSE dplyr enrichplot GO.db GOSemSim gson httr igraph magrittr methods plyr qvalue rlang stats tidyr utils yulab.utils Organism.dplyr: dplyr AnnotationFilter RSQLite S4Vectors Seqinfo IRanges GenomicRanges GenomicFeatures AnnotationDbi rlang methods tools utils BiocFileCache DBI dbplyr tibble gtable: cli glue grid lifecycle rlang stats pcaMethods: Biobase methods BiocGenerics Rcpp MASS R.methodsS3: utils ggsci: ggplot2 grDevices rlang scales TxDb.Athaliana.BioMart.plantsmart22: GenomicFeatures AnnotationDbi DESeq2: S4Vectors IRanges GenomicRanges SummarizedExperiment BiocGenerics Biobase BiocParallel matrixStats methods stats4 locfit ggplot2 Rcpp MatrixGenerics RcppArmadillo BiocVersion: geneplotter: methods Biobase BiocGenerics lattice annotate AnnotationDbi graphics grDevices grid RColorBrewer stats utils rrcov: robustbase methods stats stats4 mvtnorm lattice pcaPP car: carData abind Formula MASS mgcv nnet pbkrtest quantreg grDevices utils stats graphics lme4 nlme scales polynom: stats graphics formatR: metap: lattice Rdpack TFisher mutoss mathjaxr qqconf glmpca: MASS methods stats utils org.Mm.eg.db: methods AnnotationDbi VennDiagram: grid futile.logger methods gitcreds: otel: igraph: methods cli graphics grDevices lifecycle magrittr Matrix pkgconfig rlang stats utils vctrs cpp11 nnet: stats utils qvalue: splines ggplot2 grid reshape2 dotCall64: dir.expiry: utils filelock png: listenv: lattice: grid grDevices graphics stats utils latticeExtra: lattice grid stats utils grDevices png jpeg RColorBrewer interp MASS lmerTest: lme4 stats methods numDeriv MASS ggplot2 hgu133plus2.db: methods AnnotationDbi org.Hs.eg.db survival: graphics Matrix methods splines stats utils htmlTable: stringr knitr magrittr methods checkmate htmlwidgets htmltools rstudioapi gridGraphics: grid graphics grDevices GeoMxWorkflows: NanoStringNCTools GeomxTools Biobase S4Vectors rjson readxl EnvStats dplyr reshape2 methods utils stats data.table outliers BiocGenerics ggplot2 ggrepel ggforce cowplot scales umap Rtsne pheatmap BiocStyle networkD3 urlchecker: cli curl tools xml2 isoband: cli grid rlang utils cpp11 IlluminaHumanMethylationEPICmanifest: minfi recountWorkflow: recount GenomicRanges limma edgeR DESeq2 pheatmap regionReport clusterProfiler org.Hs.eg.db gplots derfinder GenomicState bumphunter derfinderPlot reprex: callr cli clipr fs glue knitr lifecycle rlang rmarkdown rstudioapi utils withr rngtools: methods digest utils stats parallel derfinderPlot: derfinder Seqinfo GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 graphics grDevices IRanges limma methods plyr RColorBrewer reshape2 S4Vectors scales utils foreach: codetools utils iterators progress: crayon hms prettyunits R6 PolyPhen.Hsapiens.dbSNP131: VariantAnnotation RSQLite AnnotationDbi digest: utils naivebayes: ggrepel: ggplot2 grid Rcpp rlang scales withr ff: bit utils SeuratObject: sp future future.apply generics grDevices grid lifecycle Matrix methods progressr Rcpp rlang spam stats tools utils RcppEigen RcppArmadillo: Rcpp stats utils methods TCGAWorkflowData: SummarizedExperiment here: rprojroot RTCGAToolbox: BiocGenerics data.table DelayedArray GenomicRanges Seqinfo httr methods RaggedExperiment RCurl RJSONIO rvest S4Vectors stats stringr SummarizedExperiment TCGAutils utils rtracklayer: methods GenomicRanges XML BiocGenerics S4Vectors IRanges XVector Seqinfo Biostrings curl httr Rsamtools GenomicAlignments BiocIO tools restfulr jquerylib: htmltools webshot: magrittr jsonlite callr annotate: AnnotationDbi XML Biobase DBI xtable graphics utils stats methods BiocGenerics httr fs: methods compiler: derfinder: BiocGenerics AnnotationDbi BiocParallel bumphunter derfinderHelper Seqinfo GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges methods qvalue Rsamtools rtracklayer S4Vectors stats utils timeDate: methods graphics utils stats fastmatch: impute: hwriter: CAGEWorkflow: CAGEfightR nanotubes gh: cli gitcreds glue httr2 ini jsonlite lifecycle rlang HTMLUtils: R2HTML methods grDevices memuse: methods utils InteractionSet: GenomicRanges SummarizedExperiment methods Matrix Rcpp BiocGenerics S4Vectors IRanges Seqinfo Biobase: BiocGenerics utils methods assorthead: grDevices: ncdfFlow: flowCore methods BH Biobase BiocGenerics cpp11 Rhdf5lib pracma: graphics grDevices stats utils annotatr: AnnotationDbi AnnotationHub dplyr GenomicFeatures GenomicRanges Seqinfo ggplot2 IRanges methods readr regioneR reshape2 rlang rtracklayer S4Vectors stats utils Formula: stats xts: zoo methods nloptr: BiocManager: utils filelock: waldo: cli diffobj glue methods rlang ALL: Biobase rematch: svglite: base64enc cli lifecycle rlang systemfonts textshaping cpp11 fluentGenomics: plyranges dplyr SummarizedExperiment readr stats utils gt: base64enc bigD bitops cli commonmark dplyr fs glue htmltools htmlwidgets juicyjuice magrittr markdown reactable rlang sass scales tidyselect vctrs xml2 AnnotationFilter: utils methods GenomicRanges lazyeval credentials: openssl sys curl jsonlite askpass hms: cli lifecycle methods pkgconfig rlang vctrs RcppNumerical: Rcpp RcppEigen qap: ggplot2: cli grDevices grid gtable isoband lifecycle rlang S7 scales stats vctrs withr GenomicFiles: BiocGenerics BiocParallel GenomicRanges MatrixGenerics methods Rsamtools rtracklayer SummarizedExperiment BiocBaseUtils GenomeInfoDb GenomicAlignments IRanges S4Vectors Seqinfo VariantAnnotation psych: mnormt parallel stats graphics grDevices methods lattice nlme GPArotation DEFormats: checkmate data.table DESeq2 edgeR GenomicRanges methods S4Vectors stats SummarizedExperiment arrays: lazyeval: beanplot: chipseqDBData: AnnotationHub ExperimentHub Rsamtools S4Vectors pathview: KEGGgraph XML Rgraphviz graph png AnnotationDbi org.Hs.eg.db KEGGREST methods utils RBGL: graph methods BH Rcpp: methods utils TFMPvalue: Rcpp dendextend: utils stats datasets magrittr ggplot2 viridis data.table: methods ggnewscale: ggplot2 CodeDepends: methods codetools graph XML utils affyPLM: BiocGenerics affy Biobase gcrma stats preprocessCore graphics grDevices methods hunspell: Rcpp digest snm: corpcor lme4 splines matrixStats: abind: methods utils gplots: gtools stats caTools KernSmooth methods rvest: cli glue httr lifecycle magrittr rlang selectr tibble xml2 SpatialExperiment: methods SingleCellExperiment rjson grDevices magick utils S4Vectors SummarizedExperiment BiocGenerics BiocFileCache JASPAR2016: methods shiny: methods bslib cachem cli commonmark fastmap fontawesome glue grDevices htmltools httpuv jsonlite later lifecycle mime otel promises R6 rlang sourcetools tools utils withr xtable labeling: stats graphics ordinal: stats methods ucminf MASS Matrix numDeriv nlme markdown: utils xfun litedown org.Sc.sgd.db: methods AnnotationDbi preprocessCore: stats BiocWorkflowTools: BiocStyle bookdown git2r httr knitr rmarkdown rstudioapi stringr tools utils usethis fda: splines fds deSolve cachem: rlang fastmap cigarillo: methods BiocGenerics S4Vectors IRanges Biostrings stats jsonlite: methods reformulas: stats methods Matrix Rdpack TCGAutils: AnnotationDbi BiocGenerics BiocBaseUtils GenomeInfoDb GenomicFeatures GenomicRanges GenomicDataCommons glue IRanges methods MultiAssayExperiment RaggedExperiment rvest S4Vectors Seqinfo stats stringr SummarizedExperiment utils xml2 affxparser: IDPmisc: methods grid lattice colorRamps: outliers: progressr: digest utils annotation: GenomeInfoDb VariantAnnotation AnnotationHub Organism.dplyr TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene TxDb.Mmusculus.UCSC.mm10.ensGene org.Hs.eg.db org.Mm.eg.db Homo.sapiens BSgenome.Hsapiens.UCSC.hg19 biomaRt BSgenome TxDb.Athaliana.BioMart.plantsmart22 htmlwidgets: grDevices htmltools jsonlite knitr rmarkdown yaml memoise: rlang cachem TFisher: stats sn mvtnorm Matrix fontLiberation: rainbow: MASS pcaPP hdrcde cluster colorspace ks methods fds: rainbow RCurl GSEABase: BiocGenerics Biobase annotate methods graph AnnotationDbi XML hexbin: methods lattice grid graphics grDevices stats utils future.apply: future globals parallel utils downloader: utils digest nnls: registry: utils timechange: cpp11 rstudioapi: viridis: viridisLite ggplot2 gridExtra TSP: graphics foreach utils stats grDevices systemfonts: base64enc grid jsonlite lifecycle tools utils cpp11 rafalib: RColorBrewer BiocManager RProtoBufLib: bdsmatrix: methods ks: FNN kernlab KernSmooth Matrix mclust mgcv multicool mvtnorm pracma devtools: usethis cli desc ellipsis fs lifecycle memoise miniUI pkgbuild pkgdown pkgload profvis rcmdcheck remotes rlang roxygen2 rversions sessioninfo stats testthat tools urlchecker utils withr urca: methods nlme graphics stats ExpressionNormalizationWorkflow: Biobase limma lme4 matrixStats pvca snm sva vsn ggrastr: ggplot2 Cairo ggbeeswarm grid png ragg BH: vipor: stats graphics getopt: stats BiocFileCache: dbplyr methods stats utils dplyr RSQLite DBI filelock curl httr2 ExpHunterSuite: ReactomePA limma edgeR NOISeq biomaRt topGO diffcoexp DT ggplot2 stringr WGCNA dplyr AnnotationDbi BiocGenerics enrichplot rmarkdown stats Biobase DESeq2 ROCR data.table knitr magrittr SummarizedExperiment miRBaseVersions.db grDevices graphics utils BiocParallel MKinfer matrixStats ggupset rlang plyr tidyr GO.db Matrix fastcluster DOSE heatmaply EnhancedVolcano ggrepel clusterProfiler GenomicRanges GenomicFeatures tximport annotatr ggridges FactoInvestigate FactoMineR pillar: cli glue lifecycle rlang utf8 utils vctrs ggpubr: ggplot2 ggrepel grid ggsci stats utils tidyr purrr dplyr cowplot ggsignif scales gridExtra glue polynom rlang rstatix tibble magrittr generegulation: BSgenome.Scerevisiae.UCSC.sacCer3 Biostrings GenomicFeatures MotifDb S4Vectors TxDb.Scerevisiae.UCSC.sacCer3.sgdGene motifStack org.Sc.sgd.db seqLogo rversions: curl TTR: xts zoo curl commonmark: rjson: maEndToEnd: Biobase oligoClasses ArrayExpress pd.hugene.1.0.st.v1 hugene10sttranscriptcluster.db oligo arrayQualityMetrics limma topGO ReactomePA clusterProfiler gplots ggplot2 geneplotter pheatmap RColorBrewer dplyr tidyr stringr matrixStats genefilter openxlsx Rgraphviz enrichplot leaps: VariantAnnotation: methods BiocGenerics MatrixGenerics Seqinfo GenomicRanges SummarizedExperiment Rsamtools utils DBI Biobase S4Vectors IRanges XVector Biostrings AnnotationDbi rtracklayer BSgenome GenomicFeatures curl Rhtslib IlluminaHumanMethylation450kanno.ilmn12.hg19: minfi bitops: Rdpack: methods tools utils rbibutils BiocNeighbors: Rcpp methods assorthead hdrcde: locfit ash ks KernSmooth ggplot2 RColorBrewer R.utils: R.oo methods utils tools R.methodsS3 tximeta: SummarizedExperiment tximport jsonlite S4Vectors IRanges GenomicRanges AnnotationDbi GenomicFeatures txdbmaker ensembldb BiocFileCache AnnotationHub Biostrings tibble Seqinfo tools utils methods Matrix BSgenome: methods BiocGenerics S4Vectors IRanges Seqinfo GenomicRanges Biostrings BiocIO rtracklayer utils stats matrixStats XVector Rsamtools minet: infotheo rentrez: XML httr jsonlite ggridges: ggplot2 grid scales withr cpp11: roxygen2: brew cli commonmark desc knitr methods pkgload purrr R6 rlang stringi stringr utils withr xml2 cpp11 minfi: methods BiocGenerics GenomicRanges SummarizedExperiment Biostrings bumphunter S4Vectors Seqinfo 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 shape: stats graphics grDevices evaluate: coda: lattice pander: grDevices graphics methods utils stats digest tools Rcpp RJSONIO: methods nor1mix: stats graphics IlluminaHumanMethylationEPICv2manifest: minfi utils Rhtslib: tools miRBaseVersions.db: AnnotationDbi DBI RSQLite methods gtools cli: utils pd.hugene.1.0.st.v1: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors exactRankTests: stats utils futile.options: jomo: stats lme4 survival MASS ordinal tibble gert: askpass credentials openssl rstudioapi sys zip KernSmooth: stats checkmate: backports utils DT: crosstalk htmltools htmlwidgets jquerylib jsonlite magrittr promises bigD: EGSEA123: EGSEA limma edgeR illuminaio vroom: bit64 cli crayon glue hms lifecycle methods rlang stats tibble tidyselect tzdb vctrs withr cpp11 progress ids: openssl uuid tximport: utils stats methods BiocStyle: bookdown knitr rmarkdown stats utils yaml BiocManager data.tree: R6 stringi methods venneuler: rJava stats: utils grDevices graphics singscore: methods stats graphics ggplot2 grDevices ggrepel GSEABase plotly tidyr plyr magrittr reshape edgeR RColorBrewer Biobase BiocParallel SummarizedExperiment matrixStats reshape2 S4Vectors FactoInvestigate: FactoMineR stats methods graphics rmarkdown parallel ggplot2 plyranges: BiocGenerics IRanges GenomicRanges dplyr methods rlang magrittr tidyselect rtracklayer GenomicAlignments Seqinfo Rsamtools S4Vectors utils qqman: calibrate GGally: ggplot2 cli dplyr ggstats grDevices grid gtable lifecycle magrittr progress RColorBrewer rlang S7 scales tidyr utils arrayQualityMetrics: affy affyPLM beadarray Biobase genefilter graphics grDevices grid gridSVG Hmisc hwriter lattice latticeExtra limma methods RColorBrewer setRNG stats utils vsn XML svglite lmtest: stats zoo graphics gson: jsonlite methods rlang stats tidyr utils tools: mutoss: mvtnorm plotrix multtest multcomp methods GeomxTools: Biobase NanoStringNCTools S4Vectors BiocGenerics rjson readxl EnvStats reshape2 methods utils stats data.table lmerTest dplyr stringr grDevices graphics GGally rlang ggplot2 SeuratObject gwascat: methods S4Vectors IRanges Seqinfo GenomeInfoDb GenomicRanges GenomicFeatures readr Biostrings AnnotationDbi BiocFileCache snpStats VariantAnnotation AnnotationHub data.table tibble rlang: utils MKdescr: stats graphics ggplot2 scales rlang readr: cli clipr crayon hms lifecycle methods R6 rlang tibble utils vroom cpp11 tzdb matlab: methods BSgenome.Scerevisiae.UCSC.sacCer3: BSgenome vegan: permute MASS cluster lattice mgcv ProtGenerics: methods sva: mgcv genefilter BiocParallel matrixStats stats graphics utils limma edgeR stringr: cli glue lifecycle magrittr rlang stringi vctrs fontawesome: rlang htmltools askpass: sys Rtsne: Rcpp stats caTools: bitops HDF5Array: methods SparseArray DelayedArray h5mread utils stats tools Matrix BiocGenerics S4Vectors IRanges S4Arrays rhdf5 BiocSingular: BiocGenerics S4Vectors Matrix methods utils DelayedArray BiocParallel ScaledMatrix irlba rsvd Rcpp beachmat assorthead polyclip: tzdb: cpp11 scatterpie: ggplot2 ggforce rlang ggfun stats tidyr dplyr utils yulab.utils ps: utils snpStats: survival Matrix methods graphics grDevices stats utils BiocGenerics missMethyl: IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylationEPICanno.ilm10b4.hg19 IlluminaHumanMethylationEPICv2anno.20a1.hg38 AnnotationDbi BiasedUrn Biobase BiocGenerics GenomeInfoDb GenomicRanges GO.db IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICv2manifest IRanges limma methods methylumi minfi org.Hs.eg.db ruv S4Vectors statmod stringr SummarizedExperiment mice: broom dplyr glmnet graphics grDevices lattice mitml nnet Rcpp rpart stats tidyr utils cpp11 whisker: flashClust: uwot: Matrix FNN irlba methods Rcpp RcppAnnoy RSpectra dqrng RcppProgress Rgraphviz: methods utils graph grid stats4 graphics grDevices emdbook: MASS lattice plyr coda bbmle GPArotation: stats Deriv: methods RcppProgress: gtools: methods stats utils GlobalOptions: methods utils stringi: tools utils stats numDeriv: hgu133a.db: methods AnnotationDbi org.Hs.eg.db GenomicRanges: methods stats4 BiocGenerics S4Vectors IRanges Seqinfo utils stats doBy: methods boot broom cowplot Deriv dplyr forecast ggplot2 MASS Matrix modelr microbenchmark rlang purrr tibble tidyr fdrtool: graphics grDevices stats vsn: methods Biobase affy limma lattice ggplot2 MotifDb: methods BiocGenerics S4Vectors IRanges GenomicRanges Biostrings rtracklayer splitstackshape BiocBaseUtils: methods utils Matrix: methods grDevices graphics grid lattice stats utils reactable: digest htmltools htmlwidgets jsonlite reactR RUVSeq: Biobase EDASeq edgeR methods MASS umap: Matrix methods openssl reticulate Rcpp RSpectra stats KEGGREST: methods httr png Biostrings treeio: ape dplyr jsonlite magrittr methods rlang stats tibble tidytree utils yulab.utils DiffCorr: fdrtool igraph multtest pcaMethods graphics grDevices stats utils benchmarkmeData: dplyr graphics tibble utils restfulr: methods XML RCurl rjson S4Vectors yaml rJava: methods TxDb.Mmusculus.UCSC.mm10.ensGene: GenomicFeatures AnnotationDbi universalmotif: methods stats utils MASS ggplot2 yaml IRanges Rcpp Biostrings BiocGenerics S4Vectors rlang grid MatrixGenerics RcppThread fansi: grDevices utils glmnet: Matrix methods utils foreach shape survival Rcpp RcppEigen cytofWorkflow: BiocStyle knitr readxl CATALYST diffcyt HDCytoData uwot cowplot CATALYST: SingleCellExperiment circlize ComplexHeatmap ConsensusClusterPlus cowplot data.table dplyr drc flowCore FlowSOM ggplot2 ggrepel ggridges graphics grDevices grid gridExtra Matrix matrixStats methods nnls purrr RColorBrewer reshape2 Rtsne SummarizedExperiment S4Vectors scales scater stats sn: methods stats4 mnormt numDeriv utils quantreg corpcor: stats ReactomePA: AnnotationDbi DOSE enrichplot ggplot2 ggraph reactome.db igraph graphite gson yulab.utils forecast: colorspace fracdiff generics ggplot2 graphics lmtest magrittr nnet parallel Rcpp stats timeDate tseries urca withr zoo RcppArmadillo xopen: processx sp: methods utils stats graphics grDevices lattice grid EnhancedVolcano: ggplot2 ggrepel methods scales grid grDevices c3net: igraph IlluminaHumanMethylation450kmanifest: minfi reshape: plyr Rhdf5lib: farver: oligo: BiocGenerics oligoClasses Biobase Biostrings affyio affxparser DBI ff graphics methods preprocessCore RSQLite splines stats stats4 utils bit bslib: base64enc cachem fastmap grDevices htmltools jquerylib jsonlite lifecycle memoise mime rlang sass DNAcopy: magrittr: sys: sandwich: stats utils zoo snow: utils usethis: cli clipr crayon curl desc fs gert gh glue jsonlite lifecycle purrr rappdirs rlang rprojroot rstudioapi stats tools utils whisker withr yaml base64enc: flowCore: Biobase BiocGenerics grDevices graphics methods stats utils stats4 Rcpp matrixStats cytolib S4Vectors cpp11 BH RProtoBufLib ggiraph: cli dplyr gdtools ggplot2 grid htmltools htmlwidgets purrr Rcpp rlang S7 stats systemfonts vctrs fastqcr: dplyr grid gridExtra ggplot2 magrittr readr rmarkdown rvest tibble tidyr scales stats utils xml2 rlang DelayedMatrixStats: MatrixGenerics DelayedArray methods sparseMatrixStats Matrix S4Vectors IRanges SparseArray affy: BiocGenerics Biobase affyio BiocManager graphics grDevices methods preprocessCore stats utils plotrix: grDevices graphics stats utils DEXSeq: BiocParallel Biobase SummarizedExperiment IRanges GenomicRanges DESeq2 AnnotationDbi RColorBrewer S4Vectors BiocGenerics biomaRt hwriter methods stringr Rsamtools statmod geneplotter genefilter arrangements: gmp methods R6 pwalign: BiocGenerics S4Vectors IRanges Biostrings methods utils XVector GenomicState: AnnotationHub Seqinfo GenomicFeatures rtracklayer bumphunter derfinder AnnotationDbi IRanges org.Hs.eg.db utils methods txdbmaker doRNG: foreach rngtools stats utils iterators plyr: Rcpp quantmod: xts zoo TTR methods curl jsonlite motifStack: methods grid ade4 Biostrings ggplot2 grDevices graphics htmlwidgets stats stats4 utils XML TFBSTools ggforce: ggplot2 grid scales MASS tweenr gtable rlang polyclip stats grDevices tidyselect withr utils lifecycle cli vctrs systemfonts cpp11 minfiData: minfi IlluminaHumanMethylation450kmanifest IlluminaHumanMethylation450kanno.ilmn12.hg19 future: digest globals listenv parallel parallelly utils variants: GenomeInfoDb VariantAnnotation org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene BSgenome.Hsapiens.UCSC.hg19 PolyPhen.Hsapiens.dbSNP131 haven: cli forcats hms lifecycle methods readr rlang tibble tidyselect vctrs cpp11 chipseqDB: fission: SummarizedExperiment S4Arrays: methods Matrix abind BiocGenerics S4Vectors IRanges stats TxDb.Hsapiens.UCSC.hg19.knownGene: GenomicFeatures AnnotationDbi downlit: brio desc digest evaluate fansi memoise rlang vctrs withr yaml praise: safe: AnnotationDbi Biobase methods SparseM methylumi: Biobase methods scales reshape2 ggplot2 matrixStats FDb.InfiniumMethylation.hg19 minfi BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges SummarizedExperiment graphics lattice annotate genefilter AnnotationDbi stats4 illuminaio GenomicFeatures S4Vectors: methods utils stats stats4 BiocGenerics uuid: jpeg: multtest: methods BiocGenerics Biobase survival MASS stats4 GSA: statmod: stats graphics spelling: commonmark xml2 hunspell knitr metapod: Rcpp diffcoexp: WGCNA SummarizedExperiment stats DiffCorr psych igraph BiocGenerics pbapply: parallel knitr: evaluate highr methods tools xfun yaml BiocIO: BiocGenerics S4Vectors methods tools testthat: brio callr cli desc evaluate jsonlite lifecycle magrittr methods pkgload praise processx ps R6 rlang utils waldo withr illuminaio: base64 HDCytoData: ExperimentHub SummarizedExperiment flowCore utils methods utils: 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 ShortRead: BiocGenerics BiocParallel Biostrings Rsamtools GenomicAlignments Biobase S4Vectors IRanges Seqinfo GenomicRanges pwalign hwriter methods lattice latticeExtra XVector Rhtslib nlme: graphics stats utils lattice beeswarm: stats graphics grDevices utils ConsensusClusterPlus: Biobase ALL graphics stats utils cluster UpSetR: ggplot2 gridExtra plyr utils stats methods grDevices scales ggtree: ape aplot dplyr ggplot2 grid magrittr methods purrr rlang ggfun yulab.utils tidyr tidytree treeio utils scales stats cli ggiraph rcmdcheck: callr cli curl desc digest pkgbuild prettyunits R6 rprojroot sessioninfo utils withr xopen MultiAssayExperiment: SummarizedExperiment Biobase BiocBaseUtils BiocGenerics DelayedArray GenomicRanges IRanges MatrixGenerics methods S4Vectors tidyr utils knitrBootstrap: knitr rmarkdown markdown viridisLite: reactR: htmltools selectr: methods stringr R6 aroma.light: stats R.methodsS3 R.oo R.utils matrixStats BiocGenerics: methods utils graphics stats generics DelayedArray: methods stats4 Matrix BiocGenerics MatrixGenerics S4Vectors IRanges S4Arrays SparseArray stats sparseMatrixStats: MatrixGenerics Rcpp Matrix matrixStats methods dqrng: Rcpp BH sitmo minqa: Rcpp FDb.InfiniumMethylation.hg19: GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene org.Hs.eg.db AnnotationDbi Biostrings factoextra: ggplot2 abind cluster dendextend FactoMineR ggpubr grid stats reshape2 ggrepel tidyr lifecycle: cli glue rlang pixmap: methods graphics grDevices ini: globals: codetools multcompView: grid bookdown: htmltools knitr rmarkdown jquerylib xfun tinytex yaml diffobj: crayon tools methods utils stats Seqinfo: methods BiocGenerics stats S4Vectors IRanges knitcitations: RefManageR digest httr methods utils IlluminaHumanMethylationEPICv2anno.20a1.hg38: minfi utils biomaRt: methods AnnotationDbi BiocFileCache curl httr2 progress stringr utils xml2 permute: stats TxDb.Hsapiens.UCSC.hg38.knownGene: GenomicFeatures AnnotationDbi scater: SingleCellExperiment scuttle ggplot2 stats utils methods Matrix BiocGenerics S4Vectors SummarizedExperiment MatrixGenerics SparseArray DelayedArray beachmat BiocNeighbors BiocSingular BiocParallel rlang ggbeeswarm viridis Rtsne RColorBrewer RcppML uwot pheatmap ggrepel ggrastr qqconf: MASS robustbase Rcpp miceadds: mice graphics methods mitools Rcpp stats utils RcppArmadillo dichromat: stats XML: methods utils reactome.db: methods AnnotationDbi optparse: methods getopt Glimma: htmlwidgets edgeR DESeq2 limma SummarizedExperiment stats jsonlite methods S4Vectors XVector: methods BiocGenerics S4Vectors IRanges utils stats tools magick: Rcpp magrittr curl networkD3: data.tree htmlwidgets igraph jsonlite magrittr Rsamtools: methods Seqinfo GenomicRanges Biostrings utils BiocGenerics S4Vectors IRanges XVector bitops BiocParallel stats Rhtslib bigreadr: bigassertr data.table parallelly Rcpp utils stageR: SummarizedExperiment methods stats rsvd: Matrix pvca: Matrix Biobase vsn stats lme4 kernlab: methods stats grDevices graphics carData: stats4: graphics methods stats DEoptimR: stats RefManageR: xml2 jsonlite utils plyr tools httr lubridate stringr methods bibtex plotly: ggplot2 tools scales httr jsonlite magrittr digest viridisLite base64enc htmltools htmlwidgets tidyr RColorBrewer dplyr vctrs tibble lazyeval rlang crosstalk purrr data.table promises gage: graph KEGGREST AnnotationDbi GO.db NanoStringNCTools: Biobase S4Vectors ggplot2 BiocGenerics Biostrings ggbeeswarm ggiraph ggthemes grDevices IRanges methods pheatmap RColorBrewer stats utils ensembldb: BiocGenerics GenomicRanges GenomicFeatures AnnotationFilter methods RSQLite DBI Biobase Seqinfo GenomeInfoDb AnnotationDbi rtracklayer S4Vectors Rsamtools IRanges ProtGenerics Biostrings curl RnaSeqGeneEdgeRQL: edgeR gplots org.Mm.eg.db GO.db BiocStyle org.Hs.eg.db: methods AnnotationDbi calibrate: MASS R6: mime: tools microbenchmark: graphics stats multicool: methods Rcpp reticulate: Matrix Rcpp RcppTOML graphics here jsonlite methods png rappdirs utils rlang withr genefilter: MatrixGenerics AnnotationDbi annotate Biobase graphics methods stats survival grDevices SingscoreAMLMutations: dcanr edgeR ggplot2 gridExtra GSEABase mclust org.Hs.eg.db plyr reshape2 rtracklayer singscore SummarizedExperiment TCGAbiolinks BiocFileCache mnormt: ELMER: ELMER.data GenomicRanges ggplot2 reshape grid grDevices graphics methods parallel stats utils IRanges Seqinfo 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 GenomicInteractions: InteractionSet Rsamtools rtracklayer GenomicRanges IRanges BiocGenerics data.table stringr Seqinfo ggplot2 grid gridExtra methods igraph S4Vectors dplyr Gviz Biobase graphics stats utils grDevices GSVA: methods stats utils graphics parallel BiocGenerics MatrixGenerics S4Vectors S4Arrays HDF5Array SparseArray DelayedArray IRanges Biobase SummarizedExperiment GSEABase Matrix BiocParallel SingleCellExperiment BiocSingular SpatialExperiment sparseMatrixStats cli memuse ggtangle: ggfun ggplot2 ggrepel igraph rlang yulab.utils clue: stats cluster graphics methods ade4: graphics grDevices methods stats utils MASS pixmap sp Rcpp RcppArmadillo SparseM: methods graphics stats utils DOSE: AnnotationDbi BiocParallel fgsea ggplot2 GOSemSim methods qvalue reshape2 stats utils yulab.utils gcrma: affy graphics methods stats utils Biobase affyio XVector Biostrings splines BiocManager RcppAnnoy: methods Rcpp yaml: RSQLite: bit64 blob DBI memoise methods pkgconfig rlang plogr cpp11 tidygraph: cli dplyr igraph lifecycle magrittr pillar R6 rlang stats tibble tidyr tools utils cpp11 simpleSingleCell: utils methods knitr callr rmarkdown CodeDepends BiocStyle base64: openssl S7: utils fracdiff: stats deSolve: methods graphics grDevices stats futile.logger: utils lambda.r futile.options ggstats: cli dplyr forcats ggplot2 lifecycle patchwork purrr rlang scales stats stringr utils tidyr brew: zip: EGSEA: Biobase gage AnnotationDbi topGO pathview PADOG GSVA globaltest limma edgeR HTMLUtils hwriter gplots ggplot2 safe stringi parallel stats metap grDevices graphics utils org.Hs.eg.db org.Mm.eg.db org.Rn.eg.db RColorBrewer methods EGSEAdata htmlwidgets plotly DT ChIPseeker: AnnotationDbi aplot BiocGenerics boot dplyr enrichplot IRanges GenomeInfoDb GenomicRanges GenomicFeatures ggplot2 gplots graphics grDevices gtools magrittr methods plotrix parallel RColorBrewer rlang rtracklayer S4Vectors scales stats tibble TxDb.Hsapiens.UCSC.hg19.knownGene utils yulab.utils gclus: cluster purrr: cli lifecycle magrittr rlang vctrs gridSVG: grDevices graphics utils methods grid jsonlite XML IlluminaHumanMethylationEPICanno.ilm10b4.hg19: minfi litedown: utils commonmark xfun graphite: methods AnnotationDbi graph httr rappdirs stats utils graphics rlang lifecycle purrr dir.expiry airway: SummarizedExperiment dynamicTreeCut: stats blob: methods rlang vctrs Homo.sapiens: AnnotationDbi methods OrganismDbi GenomicFeatures GO.db org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene later: Rcpp rlang tweenr: farver magrittr rlang vctrs cpp11 ggplotify: ggplot2 graphics grDevices grid gridGraphics rlang yulab.utils BiocParallel: methods stats utils futile.logger parallel snow codetools BH cpp11 scales: cli farver glue labeling lifecycle R6 RColorBrewer rlang viridisLite pryr: codetools lobstr methods Rcpp stringr httr: curl jsonlite mime openssl R6 TxDb.Mmusculus.UCSC.mm10.knownGene: GenomicFeatures AnnotationDbi mitml: pan jomo haven grDevices graphics stats methods utils