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graphics grDevices stats utils smoothie: relimp: stats utils struct: methods ontologyIndex datasets graphics stats utils knitr SummarizedExperiment S4Vectors rols GSgalgoR: cluster doParallel foreach matchingR nsga2R survival proxy stats methods STROMA4: Biobase BiocParallel cluster matrixStats stats graphics utils PANR: igraph graphics grDevices MASS methods pvclust stats utils RedeR BicARE: Biobase multtest GSEABase GO.db methods ramwas: methods filematrix graphics stats utils digest glmnet KernSmooth grDevices GenomicAlignments Rsamtools parallel biomaRt Biostrings BiocGenerics PROcess: Icens graphics grDevices stats utils RPostgreSQL: methods DBI Rdisop: Rcpp rmutil: phangorn: ape digest fastmatch generics graphics grDevices igraph Matrix methods parallel quadprog Rcpp stats utils BLMA: ROntoTools GSA PADOG limma graph stats utils parallel Biobase metafor methods smoother: TTR fastcluster: qgraph: Rcpp methods grDevices psych lavaan plyr Hmisc igraph jpeg png colorspace Matrix 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SummarizedExperiment stats tibble tidyr TCGAutils utils RBM: limma marray broom: backports dplyr generics glue lifecycle purrr rlang stringr tibble tidyr inline: methods fontLiberation: oncomix: ggplot2 ggrepel RColorBrewer mclust stats SummarizedExperiment shape: stats graphics grDevices VisiumIO: TENxIO BiocBaseUtils BiocGenerics BiocIO jsonlite methods S4Vectors SpatialExperiment SummarizedExperiment logistf: mice mgcv formula.tools Matrix scmeth: knitr rmarkdown bsseq AnnotationHub GenomicRanges reshape2 stats utils BSgenome DelayedArray annotatr SummarizedExperiment GenomeInfoDb Biostrings DT HDF5Array scTHI.data: lgr: R6 GraphAlignment: GeneGeneInteR: snpStats mvtnorm Rsamtools igraph kernlab FactoMineR IRanges GenomicRanges data.table grDevices graphics stats utils methods BSgenome.Mmusculus.UCSC.mm8: BSgenome einsum: Rcpp glue mathjaxr logging: methods nullranges: stats IRanges GenomicRanges GenomeInfoDb methods rlang S4Vectors scales InteractionSet ggplot2 grDevices plyranges data.table progress ggridges BSgenome.Mmusculus.UCSC.mm9: BSgenome mosbi: Rcpp BH xml2 methods igraph fabia RcppParallel biclust isa2 QUBIC akmbiclust RColorBrewer GOfuncR: vioplot Rcpp mapplots gtools GenomicRanges IRanges AnnotationDbi utils grDevices graphics stats enrichplot: aplot DOSE ggfun ggnewscale ggplot2 ggraph graphics grid igraph methods plyr purrr RColorBrewer reshape2 rlang stats utils scatterpie shadowtext GOSemSim magrittr ggtree yulab.utils SCArray: gdsfmt methods DelayedArray S4Vectors utils Matrix BiocParallel DelayedMatrixStats SummarizedExperiment SingleCellExperiment BiocSingular NanoStringNCTools: Biobase S4Vectors ggplot2 BiocGenerics Biostrings ggbeeswarm ggiraph ggthemes grDevices IRanges methods pheatmap RColorBrewer stats utils blimaTestingData: netZooR: igraph reticulate pandaR yarn matrixcalc RCy3 viridisLite STRINGdb Biobase GOstats AnnotationDbi matrixStats GO.db org.Hs.eg.db Matrix gplots nnet data.table vegan stats utils reshape reshape2 penalized parallel doParallel foreach ggplot2 ggdendro grid MASS assertthat tidyr methods dplyr graphics RCM: DBI RColorBrewer alabama edgeR reshape2 tseries stats VGAM ggplot2 nleqslv phyloseq tensor MASS grDevices graphics methods prettyGraphs: EGSEA: Biobase gage AnnotationDbi topGO pathview PADOG GSVA globaltest limma edgeR HTMLUtils hwriter gplots ggplot2 safe stringi parallel stats metap grDevices graphics utils org.Hs.eg.db org.Mm.eg.db org.Rn.eg.db RColorBrewer methods EGSEAdata htmlwidgets plotly DT ggkegg: ggplot2 ggraph XML igraph tidygraph BiocFileCache GetoptLong data.table dplyr magick patchwork shadowtext stringr tibble org.Hs.eg.db methods utils stats AnnotationDbi grDevices gtable tfruns: utils jsonlite base64enc yaml config magrittr whisker tidyselect rlang rstudioapi reticulate HDO.db: AnnotationDbi methods utils WGSmapp: GenomicRanges GSAR: igraph stats graphics rentrez: XML httr jsonlite sampleClassifier: MGFM MGFR annotate e1071 ggplot2 stats utils tester: rpart: graphics stats grDevices ggmanh: methods ggplot2 gdsfmt ggrepel grDevices RColorBrewer rlang scales SeqArray stats bbotk: paradox checkmate data.table lgr methods mlr3misc R6 lhs: Rcpp CircSeqAlignTk: stats tools utils R.utils methods S4Vectors rlang magrittr dplyr tidyr ggplot2 BiocGenerics Biostrings IRanges ShortRead Rsamtools Rbowtie2 Rhisat2 shiny shinyFiles shinyjs plotly parallel htmltools RCX: jsonlite plyr igraph methods EnvStats: MASS ggplot2 nortest Cairo: grDevices graphics nipals: genomicInstability: checkmate mixtools SummarizedExperiment tinytex: xfun shinycssloaders: digest glue grDevices shiny epivizrServer: methods httpuv R6 rjson mime genomeIntervals: methods intervals BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors GSCA: shiny sp gplots ggplot2 reshape2 RColorBrewer rhdf5 graphics MobilityTransformR: MSnbase xcms MetaboCoreUtils Spectra forecast: colorspace fracdiff generics ggplot2 graphics lmtest magrittr nnet parallel Rcpp stats timeDate tseries urca zoo RcppArmadillo minfiData: minfi IlluminaHumanMethylation450kmanifest IlluminaHumanMethylation450kanno.ilmn12.hg19 dpeak: methods stats utils graphics Rcpp MASS IRanges BSgenome grDevices parallel flowCHIC: methods flowCore EBImage vegan hexbin ggplot2 grid DAPAR: Biobase MSnbase DAPARdata utils highcharter foreach tensorA: stats cfdnakit: Biobase dplyr GenomicRanges GenomeInfoDb ggplot2 IRanges magrittr PSCBS QDNAseq Rsamtools utils S4Vectors stats rlang PCAN: BiocParallel grDevices stats Rattus.norvegicus: AnnotationDbi methods OrganismDbi GenomicFeatures GO.db org.Rn.eg.db TxDb.Rnorvegicus.UCSC.rn5.refGene cosmosR: CARNIVAL dorothea dplyr GSEABase igraph progress purrr rlang stringr utils visNetwork decoupleR ipred: rpart MASS survival nnet class prodlim RNAmodR: S4Vectors IRanges GenomicRanges Modstrings methods stats grDevices matrixStats BiocGenerics Biostrings BiocParallel txdbmaker GenomicFeatures GenomicAlignments GenomeInfoDb rtracklayer Rsamtools BSgenome RColorBrewer colorRamps ggplot2 Gviz reshape2 graphics ROCR rfPred: methods utils GenomeInfoDb data.table IRanges GenomicRanges parallel Rsamtools statebins: ggplot2 scales grid minionSummaryData: myvariant: VariantAnnotation httr jsonlite S4Vectors Hmisc plyr magrittr GenomeInfoDb OSAT: methods stats SNPhoodData: nnls: DBI: methods SOMbrero: igraph markdown scatterplot3d shiny grDevices graphics stats ggplot2 ggwordcloud metR interp rlang biomvRCNS: IRanges GenomicRanges Gviz methods mvtnorm beadarraySNP: methods Biobase quantsmooth BiocFHIR: DT shiny jsonlite graph tidyr visNetwork dplyr utils methods BiocBaseUtils nloptr: testthat mirbase.db: methods AnnotationDbi bacon: methods stats ggplot2 graphics BiocParallel ellipse systemPipeR: Rsamtools Biostrings ShortRead methods GenomicRanges SummarizedExperiment ggplot2 yaml stringr magrittr S4Vectors crayon BiocGenerics htmlwidgets RImmPort: plyr dplyr DBI data.table reshape2 methods sqldf tools utils RSQLite RSVSim: Biostrings GenomicRanges methods IRanges ShortRead org.Ce.eg.db: methods AnnotationDbi tidySpatialExperiment: SpatialExperiment tidySingleCellExperiment ttservice SummarizedExperiment SingleCellExperiment BiocGenerics Matrix S4Vectors methods utils pkgconfig tibble dplyr tidyr ggplot2 magrittr rlang purrr stringr vctrs tidyselect pillar cli fansi lifecycle RcppHMM: Rcpp RcppArmadillo arrayQuality: graphics grDevices grid gridBase hexbin limma marray methods RColorBrewer stats utils TCGAMethylation450k: ExperimentHub: methods BiocGenerics AnnotationHub BiocFileCache utils S4Vectors BiocManager rappdirs cleaver: methods Biostrings S4Vectors IRanges SigsPack: quadprog methods Biobase BSgenome VariantAnnotation Biostrings GenomeInfoDb GenomicRanges rtracklayer SummarizedExperiment graphics stats utils powerTCR: cubature doParallel evmix foreach magrittr methods parallel purrr stats truncdist vegan VGAM reconsi: phyloseq ks reshape2 ggplot2 stats methods graphics grDevices matrixStats Matrix countsimQC: rmarkdown edgeR DESeq2 dplyr tidyr ggplot2 grDevices tools SummarizedExperiment genefilter DT GenomeInfoDbData caTools randtests stats utils methods ragg EnsDb.Rnorvegicus.v79: ensembldb zoo: stats utils graphics grDevices lattice visNetwork: htmlwidgets htmltools jsonlite magrittr utils methods grDevices stats SIMAT: Rcpp mzR ggplot2 grid reshape2 grDevices stats utils synapterdata: synapter utils WriteXLS: utils git2r: graphics utils highcharter: htmlwidgets magrittr purrr rlist assertthat zoo dplyr tibble stringr broom xts quantmod tidyr htmltools jsonlite igraph lubridate yaml rlang rjson AWFisher: edgeR limma stats survey: grid methods Matrix survival stats graphics splines lattice minqa numDeriv mitools Rcpp RcppArmadillo miRNApath: methods epigenomix: methods Biobase S4Vectors IRanges GenomicRanges SummarizedExperiment BiocGenerics MCMCpack Rsamtools parallel GenomeInfoDb beadarray kSamples: SuppDists methods graphics stats gplots: gtools stats caTools KernSmooth methods GSALightning: Matrix data.table stats scrypt: Rcpp bugsigdbr: BiocFileCache methods vroom utils org.Xl.eg.db: methods AnnotationDbi coRdon: methods stats utils Biostrings Biobase dplyr stringr purrr ggplot2 data.table vegan: permute lattice MASS cluster mgcv sigora: stats slam oppti: limma stats reshape ggplot2 grDevices RColorBrewer pheatmap knitr methods devtools parallelDist RUnit: utils methods graphics InTAD: methods S4Vectors IRanges GenomicRanges MultiAssayExperiment SummarizedExperiment stats BiocGenerics Biobase rtracklayer parallel graphics mclust qvalue ggplot2 utils ggpubr TEKRABber: apeglm biomaRt dplyr doParallel DESeq2 foreach GenomeInfoDb magrittr Rcpp rtracklayer SCBN stats utils TOAST: EpiDISH limma nnls quadprog stats methods SummarizedExperiment corpcor doParallel parallel ggplot2 tidyr GGally idiogram: methods Biobase annotate plotrix ggbump: ggplot2 dplyr purrr tidyr pd.mapping50k.xba240: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors glue: methods ParallelLogger: snow xml2 jsonlite methods utils DirichletReg: Formula stats graphics methods maxLik snifter: basilisk reticulate irlba stats assertthat ANCOMBC: mia stats CVXR DescTools Hmisc MASS Matrix Rdpack S4Vectors SingleCellExperiment SummarizedExperiment TreeSummarizedExperiment doParallel doRNG energy foreach gtools lme4 lmerTest multcomp nloptr parallel utils DEP: ggplot2 dplyr purrr readr tibble tidyr SummarizedExperiment MSnbase limma vsn fdrtool ggrepel ComplexHeatmap RColorBrewer circlize shiny shinydashboard DT rmarkdown assertthat gridExtra grid stats imputeLCMD cluster RUVSeq: Biobase EDASeq edgeR methods MASS findpython: epistack: GenomicRanges SummarizedExperiment BiocGenerics S4Vectors IRanges graphics plotrix grDevices stats methods CoSIA: methods ExperimentHub dplyr magrittr RColorBrewer tidyr plotly stringr ggplot2 tibble org.Hs.eg.db org.Mm.eg.db org.Dr.eg.db org.Ce.eg.db org.Dm.eg.db org.Rn.eg.db AnnotationDbi biomaRt homologene annotationTools readr tidyselect stats insight: methods stats utils badger: dlstats rvcheck desc usethis PeacoQC: circlize ComplexHeatmap flowCore flowWorkspace ggplot2 grDevices grid gridExtra methods plyr stats utils geneClassifiers: utils methods stats Biobase BiocGenerics timecourse: MASS methods Biobase graphics limma marray stats ITALICS: GLAD ITALICSData oligo affxparser pd.mapping50k.xba240 DBI oligoClasses stats DEGraph: R.utils graph KEGGgraph lattice mvtnorm R.methodsS3 RBGL Rgraphviz rrcov NCIgraph BiocOncoTK: methods utils ComplexHeatmap S4Vectors bigrquery shiny stats httr rjson dplyr magrittr grid DT GenomicRanges IRanges ggplot2 SummarizedExperiment DBI GenomicFeatures curatedTCGAData scales ggpubr plyr car graph Rgraphviz MASS grDevices gRain: methods gRbase igraph stats4 broom magrittr Rcpp RcppArmadillo RcppEigen MCMCprecision: Rcpp parallel utils stats Matrix combinat RcppArmadillo RcppProgress RcppEigen DelayedRandomArray: DelayedArray methods dqrng Rcpp BH ggforce: ggplot2 Rcpp grid scales MASS tweenr gtable rlang polyclip stats grDevices tidyselect withr utils lifecycle cli vctrs systemfonts RcppEigen reprex: callr cli clipr fs glue knitr lifecycle rlang rmarkdown rstudioapi utils withr MOGAMUN: stats utils RCy3 stringr graphics grDevices RUnit BiocParallel igraph kpeaks: graphics stats utils methods GenomicDistributionsData: ExperimentHub AnnotationHub AnnotationFilter data.table utils BSgenome GenomeInfoDb GenomicFeatures GenomicRanges ensembldb EBcoexpress: EBarrays mclust minqa DFP: methods Biobase tomoda: methods stats grDevices reshape2 Rtsne umap RColorBrewer ggplot2 ggrepel SummarizedExperiment progress: crayon hms prettyunits R6 pd.genomewidesnp.5: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors pd.genomewidesnp.6: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors CoCiteStats: org.Hs.eg.db AnnotationDbi Matrix: methods grDevices graphics grid lattice stats utils pdist: methods sigFeature: biocViews nlme e1071 openxlsx pheatmap RColorBrewer Matrix SparseM graphics stats utils SummarizedExperiment BiocParallel methods devtools: usethis cli desc ellipsis fs lifecycle memoise miniUI pkgbuild pkgdown pkgload profvis rcmdcheck remotes rlang roxygen2 rversions sessioninfo stats testthat tools urlchecker utils withr cycle: Mfuzz Biobase stats bnlearn: methods trio: grDevices graphics methods stats survival utils siggenes LogicReg torch: Rcpp R6 withr rlang methods utils stats bit64 magrittr tools coro callr cli glue ellipsis desc safetensors jsonlite dada2: Rcpp methods Biostrings ggplot2 reshape2 ShortRead RcppParallel parallel IRanges XVector BiocGenerics loo: checkmate matrixStats parallel posterior stats gDNAinRNAseqData: RCurl XML ExperimentHub BiocGenerics Rsamtools SingleMoleculeFootprintingData: ExperimentHub utils Rtpca: stats dplyr tidyr Biobase methods ggplot2 pROC fdrtool splines utils tibble aws.s3: utils tools curl httr xml2 base64enc digest aws.signature NxtIRFdata: ExperimentHub BiocFileCache rtracklayer R.utils RnBeads.hg38: GenomicRanges stepNorm: marray methods MASS stats NanoporeRNASeq: ExperimentHub PCHiCdata: Chicago zenith: limma methods variancePartition EnrichmentBrowser GSEABase msigdbr Rfast ggplot2 tidyr reshape2 progress utils Rdpack stats BSgenome.Celegans.UCSC.ce10: BSgenome DepInfeR: matrixStats glmnet stats BiocParallel BSgenome.Celegans.UCSC.ce11: BSgenome DrImpute: Rcpp RcppArmadillo frmaExampleData: ExploreModelMatrix: shiny shinydashboard DT cowplot utils dplyr magrittr tidyr ggplot2 stats methods rintrojs scales tibble MASS limma S4Vectors shinyjs COTAN: stats plyr dplyr methods grDevices Matrix ggplot2 ggrepel ggthemes graphics parallel parallelly tibble tidyr BiocSingular PCAtools parallelDist ComplexHeatmap circlize grid scales RColorBrewer utils rlang Rfast stringr Seurat umap dendextend zeallot assertthat withr EWCE: RNOmni stats utils methods ewceData dplyr ggplot2 reshape2 limma stringr HGNChelper Matrix parallel SingleCellExperiment SummarizedExperiment 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GenomicFiles Gviz InteractionSet GenomicInteractions flowMap: ade4 doParallel abind reshape2 scales Matrix methods rsample: cli dplyr furrr generics glue lifecycle methods pillar purrr rlang slider tibble tidyr tidyselect vctrs TxDb.Rnorvegicus.UCSC.rn7.refGene: GenomicFeatures AnnotationDbi misc3d: grDevices graphics stats tcltk caret: ggplot2 lattice e1071 foreach grDevices methods ModelMetrics nlme plyr pROC recipes reshape2 stats stats4 utils withr consensusOV: Biobase GSVA gdata genefu limma matrixStats randomForest stats utils methods BiocParallel spatstat: spatstat.data spatstat.geom spatstat.random spatstat.explore spatstat.model spatstat.linnet utils spatstat.utils ggtree: ape aplot dplyr ggplot2 grid magrittr methods purrr rlang ggfun yulab.utils tidyr tidytree treeio utils scales stats cli granulator: cowplot e1071 epiR dplyr dtangle ggplot2 ggplotify grDevices limSolve magrittr MASS nnls parallel pheatmap purrr rlang stats tibble tidyr utils scCB2: SingleCellExperiment 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pd.hugene.1.0.st.v1: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors benchmarkme: benchmarkmeData compiler doParallel dplyr foreach graphics httr Matrix methods parallel stringr tibble utils harmony: Rcpp dplyr cowplot ggplot2 Matrix methods tibble rlang RhpcBLASctl RcppArmadillo RcppProgress RnBeads.hg19: GenomicRanges smurf: catdata glmnet graphics MASS Matrix methods mgcv parallel RColorBrewer Rcpp stats RcppArmadillo UpSetR: ggplot2 gridExtra plyr utils stats methods grDevices scales Icens: survival graphics rvest: cli glue httr lifecycle magrittr rlang selectr tibble xml2 tensorflow: config processx reticulate tfruns utils yaml grDevices tfautograph rstudioapi lifecycle VGAM: methods stats stats4 splines SCnorm: SingleCellExperiment SummarizedExperiment stats methods graphics grDevices parallel quantreg cluster moments data.table BiocParallel S4Vectors ggplot2 forcats BiocGenerics getDEE2: stats utils SummarizedExperiment htm2txt NetRep: methods foreach Rcpp statmod RhpcBLASctl abind RColorBrewer utils stats graphics grDevices BH RcppArmadillo breastCancerUPP: parmigene: RProtoBufLib: MethylMix: foreach RPMM RColorBrewer ggplot2 RCurl impute data.table limma R.matlab digest mpra: methods BiocGenerics SummarizedExperiment limma S4Vectors scales stats graphics statmod hicVennDiagram: GenomeInfoDb GenomicRanges IRanges InteractionSet rtracklayer ggplot2 ComplexUpset reshape2 eulerr S4Vectors methods utils htmlwidgets svglite RegionalST: stats grDevices utils ggplot2 dplyr scater gridExtra BayesSpace fgsea magrittr SingleCellExperiment RColorBrewer Seurat S4Vectors tibble TOAST assertthat colorspace shiny SummarizedExperiment mosaics: methods graphics Rcpp MASS splines lattice IRanges GenomicRanges GenomicAlignments Rsamtools GenomeInfoDb S4Vectors lsa: SnowballC TRONCO: bnlearn Rgraphviz gtools parallel foreach doParallel iterators RColorBrewer circlize igraph grid gridExtra xtable gtable scales R.matlab grDevices graphics stats utils methods DNAshapeR: GenomicRanges Rcpp Biostrings fields oligoClasses: BiocGenerics Biobase methods graphics IRanges GenomicRanges SummarizedExperiment Biostrings affyio foreach BiocManager utils S4Vectors RSQLite DBI ff coMET: grid utils biomaRt Gviz psych hash grDevices gridExtra rtracklayer IRanges S4Vectors GenomicRanges stats corrplot scReClassify: randomForest e1071 stats SummarizedExperiment SingleCellExperiment methods nnTensor: methods MASS fields rTensor plot3D tagcloud ggplot2 signatureSearch: Rcpp SummarizedExperiment org.Hs.eg.db AnnotationDbi ggplot2 data.table ExperimentHub HDF5Array magrittr RSQLite dplyr fgsea scales methods qvalue stats utils reshape2 visNetwork BiocParallel fastmatch reactome.db Matrix clusterProfiler readr DOSE rhdf5 GSEABase DelayedArray BiocGenerics tibble timeDate: methods graphics utils stats magick: Rcpp magrittr curl RNeXML: ape methods XML plyr reshape2 httr uuid dplyr tidyr stringr stringi xml2 rlang survMisc: survival graphics grDevices stats utils knitr KMsurv ggplot2 data.table zoo grid gridExtra km.ci xtable Anaquin: ggplot2 ROCR knitr qvalue locfit methods stats utils plyr DESeq2 mco: ROC: utils methods knitr IntOMICS: bnlearn bnstruct matrixStats RColorBrewer bestNormalize igraph gplots stats utils graphics numbers SummarizedExperiment ggplot2 ggraph methods cowplot grid rlang lsr: graphics grDevices methods stats RefManageR: xml2 jsonlite utils plyr tools httr lubridate stringr methods bibtex TxDb.Athaliana.BioMart.plantsmart22: GenomicFeatures AnnotationDbi messina: survival methods Rcpp plyr ggplot2 grid foreach graphics octad.db: ExperimentHub ROI: methods registry slam utils checkmate common: utils TxDb.Athaliana.BioMart.plantsmart28: GenomicFeatures AnnotationDbi prebsdata: switchde: SingleCellExperiment SummarizedExperiment dplyr ggplot2 methods stats NPARC: dplyr tidyr BiocParallel broom MASS rlang magrittr stats methods methodical: GenomicRanges ggplot2 SummarizedExperiment BiocParallel Biostrings BSgenome cowplot data.table DelayedArray dplyr ExperimentHub foreach GenomeInfoDb HDF5Array IRanges R.utils RcppRoll rhdf5 rtracklayer S4Vectors scales tibble tidyr evobiR: seqinr ape geiger shiny phytools kriging: RedisParam: BiocParallel methods redux withr futile.logger tRanslatome: methods limma anota DESeq2 edgeR RankProd topGO org.Hs.eg.db GOSemSim Heatplus gplots plotrix Biobase MEEBOdata: iSEEpathways: iSEE ggplot2 methods S4Vectors shiny shinyWidgets stats SummarizedExperiment RPA: affy BiocGenerics BiocStyle methods rmarkdown phyloseq TPP2D: stats utils dplyr methods ggplot2 tidyr foreach doParallel openxlsx stringr RCurl parallel MASS BiocParallel limma esATAC: Rsamtools GenomicRanges ShortRead pipeFrame Rcpp methods knitr Rbowtie2 rtracklayer ggplot2 Biostrings ChIPseeker clusterProfiler igraph rJava magrittr digest BSgenome AnnotationDbi GenomicAlignments GenomicFeatures R.utils GenomeInfoDb BiocGenerics S4Vectors IRanges rmarkdown tools VennDiagram grid JASPAR2018 TFBSTools grDevices graphics stats utils parallel corrplot BiocManager motifmatchr MonoPoly: quadprog mdp: ggplot2 gridExtra grid stats utils sysfonts: breakaway: ggplot2 graphics lme4 magrittr MASS phyloseq stats tibble utils iSEEu: iSEE iSEEhex methods S4Vectors IRanges shiny SummarizedExperiment SingleCellExperiment ggplot2 DT stats colourpicker shinyAce rngWELL: survivalAnalysis: grDevices graphics stats utils survival rlang dplyr forcats magrittr purrr stringr tibble tidyr gridExtra ggplot2 scales survminer cowplot tidytidbits phytools: ape maps clusterGeneration coda combinat doParallel expm foreach graphics grDevices MASS methods mnormt nlme numDeriv optimParallel parallel phangorn scatterplot3d stats utils CNVgears: data.table ggplot2 MANOR: GLAD graphics grDevices stats utils GEOexplorer: shiny limma Biobase plotly enrichR DT XML httr sva xfun edgeR htmltools factoextra heatmaply pheatmap scales shinyHeatmaply shinybusy ggplot2 stringr umap GEOquery impute grDevices stats graphics markdown knitr 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stats stringr tibble tidyr utils zeallot RcppArmadillo RcppProgress BH fpc: MASS cluster mclust flexmix prabclus class diptest robustbase kernlab grDevices graphics methods stats utils parallel jpeg: hgu133a.db: methods AnnotationDbi org.Hs.eg.db seqcombo: ggplot2 grid igraph utils yulab.utils operator.tools: utils crisprBowtie: methods BiocGenerics Biostrings BSgenome crisprBase GenomeInfoDb GenomicRanges IRanges Rbowtie readr stats stringr utils speedglm: Matrix MASS biglm methods stats CINdex: GenomicRanges bitops gplots grDevices som dplyr gridExtra png stringr S4Vectors IRanges GenomeInfoDb graphics stats utils multiClust: mclust ctc survival cluster dendextend amap graphics grDevices NBAMSeq: SummarizedExperiment S4Vectors DESeq2 mgcv BiocParallel genefilter methods stats easylift: GenomicRanges BiocFileCache rtracklayer GenomeInfoDb R.utils tools methods GEWIST: car a4Core: Biobase glmnet methods stats BSgenome.Mmusculus.UCSC.mm10: BSgenome IntEREst: GenomicRanges Rsamtools 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S4Vectors GenomicRanges IRanges InteractionSet vroom basilisk reticulate rmarkdown rmdformats plotly dplyr stringr sessioninfo utils ggm: methods BiocManager graph igraph proteinProfiles: graphics stats BSgenome.Rnorvegicus.UCSC.rn5.masked: BSgenome BSgenome.Rnorvegicus.UCSC.rn5 KnowSeq: cqn stringr methods ggplot2 jsonlite kernlab rlist rmarkdown reshape2 e1071 randomForest caret XML praznik R.utils httr sva edgeR limma grDevices graphics stats utils Hmisc gridExtra epiNEM: BoolNet e1071 gtools stats igraph utils lattice latticeExtra RColorBrewer pcalg minet grDevices graph mnem latex2exp Xeva: methods stats utils BBmisc Biobase grDevices ggplot2 scales ComplexHeatmap parallel doParallel Rmisc grid nlme PharmacoGx downloader transport: grDevices graphics methods stats Rcpp data.table RcppEigen LSD: ScaledMatrix: methods Matrix S4Vectors DelayedArray annmap: methods GenomicRanges DBI RMySQL digest Biobase grid lattice Rsamtools genefilter IRanges BiocGenerics funtooNorm: pls 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grid ensembldb gridExtra IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylationEPICanno.ilm10b2.hg19 ggrepel ggtreeExtra: ggplot2 utils rlang ggnewscale stats ggtree tidytree cli magrittr HardyWeinberg: mice nnet Rsolnp shape Rcpp cn.mops: methods utils stats graphics parallel GenomicRanges BiocGenerics Biobase IRanges Rsamtools GenomeInfoDb S4Vectors lisaClust: ggplot2 class concaveman grid BiocParallel spatstat.explore spatstat.geom BiocGenerics S4Vectors methods spicyR purrr stats data.table dplyr tidyr SingleCellExperiment SpatialExperiment SummarizedExperiment pheatmap spatstat.random BioTIP: igraph cluster psych stringr GenomicRanges MASS scran survivalsvm: survival pracma quadprog kernlab Matrix stats Hmisc ggpubr: ggplot2 ggrepel grid ggsci stats utils tidyr purrr dplyr cowplot ggsignif scales gridExtra glue polynom rlang rstatix tibble magrittr netSmooth: scater clusterExperiment entropy 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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 miRNAtap: AnnotationDbi DBI RSQLite stringr sqldf plyr methods ndexr: RCX httr jsonlite plyr tidyr FANTOM3and4CAGE: spdl: RcppSpdlog interp: Rcpp deldir RcppEigen decoupleR: BiocParallel broom dplyr magrittr Matrix parallelly purrr rlang stats stringr tibble tidyr tidyselect withr gridtext: curl grid grDevices markdown rlang Rcpp png jpeg stringr xml2 emmeans: estimability graphics methods numDeriv stats utils mvtnorm hms: lifecycle methods pkgconfig rlang vctrs ginmappeR: KEGGREST UniProt.ws XML rentrez httr utils memoise cachem xfun: grDevices stats tools REBET: ASSET stats utils TFutils: methods dplyr magrittr miniUI shiny Rsamtools GSEABase rjson BiocFileCache DT httr readxl AnnotationDbi 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janitor limma lme4 magrittr MASS mixOmics randomForest RankProd rlang SummarizedExperiment sva tibble tidyr utils uwot vegan RNAmodR.Data: ExperimentHub ExperimentHubData utils EGAD: gplots Biobase GEOquery limma impute RColorBrewer zoo igraph plyr MASS RCurl methods svgPanZoom: htmlwidgets macrophage: fission: SummarizedExperiment miRcomp: Biobase miRcompData utils methods graphics KernSmooth stats fgsea: Rcpp data.table BiocParallel stats ggplot2 cowplot grid fastmatch Matrix scales utils BH survival: graphics Matrix methods splines stats utils GenProSeq: keras mclust tensorflow word2vec DeepPINCS ttgsea CatEncoders reticulate stats mitools: DBI methods stats scaeData: ExperimentHub rpart.plot: rpart flexclust: graphics grid lattice modeltools methods parallel stats stats4 class FScanR: stats escheR: ggplot2 SpatialExperiment SingleCellExperiment rlang SummarizedExperiment rsvd: Matrix AnVILPublish: AnVIL BiocBaseUtils BiocManager httr jsonlite rmarkdown yaml readr whisker tools utils stats seriation: ca cluster colorspace foreach gclus grDevices grid MASS qap registry stats TSP vegan MultiMed: ABarray: Biobase graphics grDevices methods multtest stats tcltk utils gageData: target: BiocGenerics GenomicRanges IRanges matrixStats methods stats graphics shiny ropls: Biobase ggplot2 graphics grDevices methods plotly stats MultiAssayExperiment MultiDataSet SummarizedExperiment utils BloodGen3Module: SummarizedExperiment ExperimentHub methods grid graphics stats grDevices circlize testthat ComplexHeatmap ggplot2 matrixStats gtools reshape2 preprocessCore randomcoloR V8 limma alabaster.se: SummarizedExperiment alabaster.base methods alabaster.ranges alabaster.matrix BiocGenerics S4Vectors IRanges GenomicRanges jsonlite rsvg: Voyager: SpatialFeatureExperiment BiocParallel bluster ggnewscale ggplot2 grDevices grid lifecycle Matrix matrixStats memuse methods patchwork rlang RSpectra S4Vectors scales scico sf SingleCellExperiment SpatialExperiment spdep stats SummarizedExperiment terra utils openEBGM: data.table ggplot2 stats lwgeom: Rcpp units sf seqCAT: GenomicRanges VariantAnnotation dplyr GenomeInfoDb ggplot2 grid IRanges methods rtracklayer rlang scales S4Vectors stats SummarizedExperiment tidyr utils minet: infotheo systemPipeTools: DESeq2 GGally Rtsne SummarizedExperiment ape dplyr ggplot2 ggrepel ggtree glmpca pheatmap plotly tibble magrittr DT stats ImmuneSpaceR: utils R6 data.table curl httr Rlabkey Biobase pheatmap ggplot2 scales stats gplots plotly heatmaply jsonlite rmarkdown preprocessCore flowCore flowWorkspace digest sangeranalyseR: stringr ape Biostrings pwalign DECIPHER parallel reshape2 sangerseqR gridExtra shiny shinydashboard shinyjs data.table plotly DT zeallot excelR shinycssloaders ggdendro shinyWidgets openxlsx tools rmarkdown knitr seqinr BiocStyle logger OmaDB: httr plyr utils ape Biostrings GenomicRanges IRanges methods topGO jsonlite ompBAM: utils Rcpp zlibbioc 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 proActiv: AnnotationDbi BiocParallel data.table dplyr DESeq2 IRanges GenomicRanges GenomicFeatures GenomicAlignments GenomeInfoDb ggplot2 gplots graphics methods rlang scales S4Vectors SummarizedExperiment stats tibble txdbmaker crmn: pcaMethods Biobase methods openxlsx: grDevices methods Rcpp stats stringi utils zip ggsci: ggplot2 grDevices scales rmeta: grid stats graphics rnaseqcomp: RColorBrewer methods RcppDist: Rcpp RcppArmadillo RNOmni: plyr Rcpp stats RcppArmadillo tpSVG: mgcv stats BiocParallel MatrixGenerics methods SingleCellExperiment SummarizedExperiment SpatialExperiment MinimumDistance: VanillaICE methods BiocGenerics MatrixGenerics Biobase S4Vectors IRanges GenomeInfoDb GenomicRanges SummarizedExperiment oligoClasses DNAcopy ff foreach matrixStats lattice data.table grid stats utils MoleculeExperiment: SpatialExperiment Matrix purrr data.table dplyr magrittr rjson utils methods terra ggplot2 rlang cli EBImage rhdf5 BiocParallel S4Vectors RcwlPipelines: Rcwl BiocFileCache rappdirs methods utils git2r httr S4Vectors numbers: hunspell: Rcpp digest RiboCrypt: ORFik bslib BiocGenerics BiocParallel Biostrings data.table dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 htmlwidgets httr IRanges jsonlite knitr markdown NGLVieweR plotly rlang RCurl shiny shinycssloaders shinyhelper shinyjqui stringr fit.models: lattice stats RESOLVE: Biostrings BSgenome BSgenome.Hsapiens.1000genomes.hs37d5 data.table GenomeInfoDb GenomicRanges glmnet ggplot2 gridExtra IRanges lsa MutationalPatterns nnls parallel reshape2 S4Vectors Qtlizer: httr curl GenomicRanges stringi 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 labdsv: mgcv cluster Rtsne MASS nethet: glasso mvtnorm GeneNet huge CompQuadForm ggm mclust parallel GSA limma multtest ICSNP glmnet network ggplot2 grDevices graphics stats utils matrixTests: matrixStats SpikeIn: affy rgoslin: Rcpp dplyr hdrcde: locfit ash ks KernSmooth ggplot2 RColorBrewer reportROC: pROC vcd methods interactiveDisplayBase: methods BiocGenerics shiny DT iASeq: graphics grDevices