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Category GOstats limma lattice AnnotationDbi edgeR annotate PFAM.db GSEABase BiocGenerics grid XML R.utils DESeq2 ggplot2 ggbio IRanges smurf: catdata glmnet graphics MASS Matrix methods mgcv parallel RColorBrewer Rcpp speedglm stats RcppArmadillo 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 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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 InteractionSet 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 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 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 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BiocGenerics SummarizedExperiment S4Vectors extraDistr openxlsx: grDevices methods Rcpp stats utils zip stringi assertive.data: assertive.base assertive.strings mco: minet: infotheo GenomicTools: gMWT Rcpp data.table GenomicTools.fileHandler circlize stringr snpStats RcppArmadillo BSgenome.Scerevisiae.UCSC.sacCer1: BSgenome MSstatsPTM: dplyr gridExtra stringr stats ggplot2 grDevices MSstatsTMT MSstatsConvert MSstats data.table Rcpp Biostrings checkmate ggrepel BSgenome.Scerevisiae.UCSC.sacCer2: BSgenome GateFinder: splancs mvoutlier methods stats diptest flowCore flowFP lsr: graphics grDevices methods stats BSgenome.Scerevisiae.UCSC.sacCer3: BSgenome shinybusy: htmltools shiny jsonlite htmlwidgets 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 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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 mirTarRnaSeq: purrr MASS pscl assertthat caTools dplyr pheatmap reshape2 corrplot grDevices graphics stats utils data.table R.utils 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 concaveman: V8 sf magrittr jsonlite dplyr tokenizers: stringi Rcpp SnowballC whisker: TarSeqQC: methods GenomicRanges Rsamtools ggplot2 plyr openxlsx grDevices stats utils S4Vectors IRanges BiocGenerics reshape2 GenomeInfoDb BiocParallel Biostrings cowplot graphics GenomicAlignments Hmisc warp: 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 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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 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stats rmio: HiddenMarkov: ISAnalytics: magrittr utils reactable htmltools dplyr readr tidyr purrr rlang tibble BiocParallel stringr fs zip lubridate lifecycle ggplot2 ggrepel stats upsetjs psych grDevices data.table readxl tools Rcapture plotly 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 stats KEGGREST propr: methods fastcluster ggplot2 grDevices igraph Rcpp stats utils aod: methods stats LACE: data.tree graphics grDevices igraph parallel RColorBrewer Rfast stats SummarizedExperiment utils pcaPP: mvtnorm bluster: stats methods utils cluster 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 quanteda: methods fastmatch magrittr Matrix Rcpp RcppParallel SnowballC stopwords stringi xml2 yaml RcppArmadillo 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 ggtree 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 purrr 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 MatrixModels: stats methods Matrix DelayedMatrixStats: MatrixGenerics DelayedArray methods matrixStats sparseMatrixStats Matrix S4Vectors IRanges 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 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 MPINet: BiasedUrn mgcv 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 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 geometry: magic Rcpp lpSolve linprog RcppProgress mutoss: mvtnorm plotrix multtest multcomp methods trackViewer: grDevices methods GenomicRanges grid Rcpp GenomeInfoDb GenomicAlignments GenomicFeatures Gviz Rsamtools S4Vectors rtracklayer BiocGenerics scales tools IRanges AnnotationDbi grImport htmlwidgets plotrix Rgraphviz InteractionSet graph utils rhdf5 ClusterJudge: stats utils graphics infotheo lattice latticeExtra httr jsonlite ash: BWStest: memoise Rcpp scTHI: BiocParallel Rtsne grDevices graphics stats glpkAPI: methods RSQLite: bit64 blob DBI memoise methods pkgconfig Rcpp plogr breakpointR: GenomicRanges cowplot breakpointRdata methods utils grDevices stats S4Vectors GenomeInfoDb IRanges Rsamtools GenomicAlignments ggplot2 BiocGenerics gtools doParallel foreach hgu133atagcdf: utils AnnotationDbi metaMA: limma SMVar 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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 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 filelock 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: 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 Rgraphviz 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: 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magrittr methods rlang tibble tidyr tidyselect peakPantheR: foreach doParallel ggplot2 gridExtra MSnbase mzR stringr methods XML minpack.lm scales shiny shinythemes shinycssloaders DT pracma utils mixtools: kernlab MASS segmented stats survival PhyloProfile: ape bioDist BiocStyle Biostrings colourpicker data.table DT energy ExperimentHub ggplot2 gridExtra pbapply RColorBrewer RCurl 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 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fastmatch ggplot2 ggrepel graphics grDevices highcharter htmltools httr jsonlite limma pairsD3 plyr purrr Rcpp recount Rfast R.utils reshape2 shinyjs stringr stats SummarizedExperiment survival tools utils XML xtable methods dtangle: DEoptimR 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 KernSmooth graphics parallel matrixStats DNAcopy stats SummarizedExperiment pls: grDevices graphics methods stats Rmpi: parallel PharmacoGx: CoreGx BiocGenerics Biobase S4Vectors SummarizedExperiment MultiAssayExperiment BiocParallel ggplot2 magicaxis RColorBrewer parallel caTools methods downloader stats utils graphics grDevices reshape2 jsonlite data.table glue units: Rcpp DelayedRandomArray: DelayedArray methods dqrng Rcpp BH plot3D: misc3d stats graphics grDevices methods RcisTarget: AUCell BiocGenerics data.table feather graphics GenomeInfoDb GenomicRanges arrow dplyr tibble GSEABase methods R.utils stats SummarizedExperiment utils metapod: Rcpp 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 XML utils annotate graph Biobase RBGL hypergraph AnnotationDbi org.At.tair.db: methods AnnotationDbi Pi: igraph dnet ggplot2 graphics Matrix GenomicRanges GenomeInfoDb supraHex scales grDevices ggrepel ROCR randomForest glmnet lattice caret plot3D stats methods MASS IRanges BiocGenerics dplyr tidyr ggnetwork osfr RCircos purrr readr tibble RMSNumpress: Rcpp iterativeBMAsurv: BMA leaps survival splines graphics grDevices stats utils DropletUtils: SingleCellExperiment utils stats methods Matrix Rcpp BiocGenerics S4Vectors SummarizedExperiment BiocParallel DelayedArray DelayedMatrixStats 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 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httr rapiclient tibble tidyselect tidyr rlang BiocManager changepoint: methods stats zoo formula.tools: operator.tools utils methods NanoStringDiff: Biobase matrixStats methods Rcpp runibic: biclust SummarizedExperiment Rcpp testthat methods catdata: MASS 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: BiocParallel MSnbase mzR methods Biobase 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 bnem: CellNOptR matrixStats snowfall Rgraphviz cluster flexclust stats RColorBrewer epiNEM mnem Biobase methods utils graphics graph affy binom limma sva vsn rmarkdown rapiclient: jsonlite httr yaml HGC: Rcpp RcppEigen Matrix RANN ape dendextend ggplot2 mclust patchwork dplyr grDevices methods stats 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 DESeq2 ggrepel SummarizedExperiment Rsubread stats ggplot2 methods rtracklayer ensembldb 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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 scico: grDevices cellmigRation: methods foreach tiff graphics stats utils reshape2 parallel doParallel grDevices matrixStats FME SpatialTools sp vioplot FactoMineR Hmisc 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 pd.huex.1.0.st.v2: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors bigrquery: assertthat bit64 curl DBI gargle glue httr lifecycle jsonlite methods prettyunits progress Rcpp rlang tibble rapidjsonr TBSignatureProfiler: ASSIGN GSVA singscore methods ComplexHeatmap RColorBrewer ggplot2 S4Vectors reshape2 ROCit DESeq2 DT edgeR gdata SummarizedExperiment magrittr stats rlang BiocParallel BiocGenerics 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: 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 SNFtool: ExPosition alluvial parsedate: rematch2 awst: stats methods SummarizedExperiment lmdme: pls stemHypoxia stats methods limma singleCellTK: SummarizedExperiment SingleCellExperiment DelayedArray Biobase ape batchelor BiocParallel celldex 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 shinyjs SingleR sva reshape2 AnnotationDbi shinyalert circlize enrichR celda shinycssloaders uwot DropletUtils scds reticulate tools tximport fishpond withr GSEABase R.utils zinbwave scRNAseq TENxPBMCData yaml rmarkdown magrittr scDblFinder metap 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 yeastNagalakshmi: ABarray: Biobase graphics grDevices methods multtest stats tcltk utils vdiffr: diffobj glue grDevices htmltools lifecycle rlang testthat xml2 cpp11 anocva: cluster 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 stats methods arrayMvout: tools methods utils parody Biobase affy mdqc affyContam lumi drosophila2probe: AnnotationDbi xmapbridge: methods EmpiricalBrownsMethod: HelloRangesData: RhpcBLASctl: seqsetvis: ggplot2 data.table eulerr GenomeInfoDb GenomicAlignments GenomicRanges ggplotify grDevices grid IRanges limma methods pbapply pbmcapply png RColorBrewer Rsamtools rtracklayer S4Vectors stats UpSetR biocthis: BiocManager fs glue rlang styler usethis PMA: flowClean: flowCore bit changepoint sfsmisc ChIC: spp ChIC.data caTools methods GenomicRanges IRanges parallel progress randomForest caret grDevices stats utils graphics S4Vectors BiocGenerics genomeIntervals Rsamtools 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 grDevices methods RColorBrewer Rhtslib survival zlibbioc listenv: tidytext: dplyr generics hunspell janeaustenr lifecycle Matrix methods purrr rlang stringr tibble tokenizers 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 supersigs: assertthat caret dplyr tidyr rsample methods rlang utils Biostrings stats SummarizedExperiment 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 jquerylib methods stringr mnormt: tmvnsim glmmTMB: methods TMB lme4 Matrix nlme numDeriv 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 distances: stats 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 timecoursedata: SummarizedExperiment 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 tricycle: SingleCellExperiment methods circular ggplot2 AnnotationDbi scater GenomicRanges IRanges S4Vectors scattermore dplyr RColorBrewer grDevices stats SummarizedExperiment utils 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 S4Vectors methods tools 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 ggformula: ggplot2 ggstance scales ggridges mosaicCore rlang magrittr tibble stringr ggforce grid labelled regsplice: glmnet SummarizedExperiment S4Vectors limma edgeR stats pbapply utils methods 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