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plotly APL: Matrix RSpectra ggrepel ggplot2 viridisLite plotly SeuratObject SingleCellExperiment magrittr SummarizedExperiment topGO methods stats utils org.Hs.eg.db org.Mm.eg.db rlang cghMCR: methods DNAcopy CNTools limma BiocGenerics stats4 rGenomeTracksData: AnnotationHub R2HTML: stats graphics utils grDevices methods rpx: methods BiocFileCache jsonlite xml2 RCurl curl utils recoup: GenomicRanges GenomicAlignments ggplot2 ComplexHeatmap BiocGenerics biomaRt Biostrings circlize GenomeInfoDb GenomicFeatures graphics grDevices httr IRanges methods parallel RSQLite Rsamtools rtracklayer S4Vectors stats stringr txdbmaker utils bioassayR: DBI RSQLite methods Matrix rjson BiocGenerics XML ChemmineR intergraph: network igraph utils rrBLUP: stats graphics grDevices parallel scRNAseq: SingleCellExperiment utils methods Matrix BiocGenerics S4Vectors SparseArray DelayedArray GenomicRanges SummarizedExperiment ExperimentHub AnnotationHub AnnotationDbi ensembldb GenomicFeatures alabaster.base alabaster.matrix alabaster.sce gypsum jsonlite DBI RSQLite MotifPeeker: BiocFileCache BiocParallel DT ggplot2 plotly universalmotif GenomicRanges IRanges rtracklayer tools htmltools rmarkdown viridis SummarizedExperiment htmlwidgets Rsamtools GenomicAlignments GenomeInfoDb Biostrings BSgenome memes S4Vectors dplyr purrr tidyr heatmaply stats utils lokern: grDevices graphics stats utils sfsmisc flowTrans: flowCore flowViz flowClust methods stats SC3: graphics stats utils methods e1071 parallel foreach doParallel doRNG shiny ggplot2 pheatmap ROCR robustbase rrcov cluster WriteXLS Rcpp SummarizedExperiment SingleCellExperiment BiocGenerics S4Vectors RcppArmadillo tcltk2: tcltk odseq: msa kebabs mclust rqt: SummarizedExperiment stats Matrix ropls methods car RUnit metap CompQuadForm glmnet utils pls showimage: png tools fftw: caret: ggplot2 lattice e1071 foreach grDevices methods ModelMetrics nlme plyr pROC recipes reshape2 stats stats4 utils withr entropy: FSelector: digest entropy randomForest RWeka CDFt: stats openPrimeR: Biostrings pwalign XML scales reshape2 seqinr IRanges GenomicRanges ggplot2 plyr dplyr stringdist stringr RColorBrewer DECIPHER lpSolveAPI digest Hmisc ape BiocGenerics S4Vectors foreach magrittr uniqtag openxlsx grid grDevices stats utils methods rlist: yaml jsonlite XML data.table CaDrA: doParallel ggplot2 gplots graphics grid gtable knnmi MASS methods misc3d plyr ppcor R.cache reshape2 stats SummarizedExperiment CAGEr: methods MultiAssayExperiment BiocGenerics BiocParallel Biostrings BSgenome CAGEfightR data.table formula.tools GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gtools IRanges KernSmooth memoise plyr rlang Rsamtools reshape2 rtracklayer S4Vectors scales som stringdist stringi SummarizedExperiment utils vegan VGAM PhenStat: SmoothWin methods car nlme nortest MASS msgps logistf knitr tools pingr ggplot2 reshape corrplot graph lme4 graphics grDevices utils stats CTdata: ExperimentHub utils arm: MASS Matrix stats lme4 abind coda graphics grDevices methods nlme utils CNORfeeder: CellNOptR graph PerformanceAnalytics: xts methods quadprog zoo rsm: estimability qPLEXanalyzer: Biobase MSnbase assertthat BiocGenerics Biostrings dplyr ggdendro ggplot2 graphics grDevices IRanges limma magrittr preprocessCore purrr RColorBrewer readr rlang scales stats stringr tibble tidyr tidyselect utils fgga: RBGL graph stats e1071 methods gRbase jsonlite BiocFileCache curl igraph similaRpeak: R6 stats h5vc: grid gridExtra ggplot2 rhdf5 reshape S4Vectors IRanges Biostrings Rsamtools methods GenomicRanges abind BiocParallel BatchJobs h5vcData GenomeInfoDb Rhtslib archive: cli glue rlang tibble scp: QFeatures IHW ggplot2 ggrepel matrixStats metapod methods MsCoreUtils MultiAssayExperiment nipals RColorBrewer S4Vectors SingleCellExperiment SummarizedExperiment stats utils r2glmm: mgcv lmerTest Matrix pbkrtest ggplot2 afex stats MASS gridExtra grid data.table dplyr rsq: methods stats MASS lme4 nlme Deriv Matrix deming mcr sda: entropy corpcor fdrtool graphics stats utils LymphoSeqDB: visdat: ggplot2 tidyr dplyr purrr readr magrittr stats tibble glue forcats cli scales scs: pd.huex.1.0.st.v2: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors deepSNV: methods graphics parallel IRanges GenomicRanges SummarizedExperiment Biostrings VGAM VariantAnnotation Rhtslib SIMAT: Rcpp mzR ggplot2 grid reshape2 grDevices stats utils cytofQC: CATALYST flowCore e1071 EZtune gbm ggplot2 hrbrthemes matrixStats randomForest rmarkdown SingleCellExperiment stats SummarizedExperiment ssc S4Vectors graphics methods targetscan.Hs.eg.db: methods AnnotationDbi ClassifyR: generics methods S4Vectors MultiAssayExperiment BiocParallel survival grid genefilter utils dplyr tidyr rlang ranger ggplot2 ggpubr reshape2 ggupset broom dcanr ash: fabricatr: rlang DIAlignR: methods stats zoo data.table magrittr dplyr tidyr rlang mzR signal bit64 reticulate ggplot2 RSQLite DBI ape phangorn pracma RMSNumpress Rcpp RcppEigen SQLDataFrame: DelayedArray S4Vectors stats utils methods BiocGenerics RSQLite duckdb DBI blacksheepr: grid stats grDevices utils circlize viridis RColorBrewer ComplexHeatmap SummarizedExperiment pasilla sendmailR: base64enc Rbwa: vroom: bit64 cli crayon glue hms lifecycle methods rlang stats tibble tidyselect tzdb vctrs withr cpp11 progress C50: Cubist partykit RTN: methods RedeR minet viper mixtools snow stats limma data.table IRanges igraph S4Vectors SummarizedExperiment car pwr pheatmap grDevices graphics utils LogicReg: survival stats graphics utils grDevices tximport: utils stats methods IntEREst: GenomicRanges Rsamtools SummarizedExperiment edgeR S4Vectors GenomicFiles seqLogo Biostrings GenomicFeatures txdbmaker IRanges seqinr graphics grDevices stats utils grid methods DBI RMariaDB GenomicAlignments BiocParallel BiocGenerics DEXSeq DESeq2 TOAST: EpiDISH limma nnls quadprog stats methods SummarizedExperiment corpcor doParallel parallel ggplot2 tidyr GGally shinytitle: shiny MODA: grDevices graphics stats utils WGCNA dynamicTreeCut igraph cluster AMOUNTAIN RColorBrewer SingleCellMultiModal: MultiAssayExperiment AnnotationHub BiocBaseUtils BiocFileCache ExperimentHub graphics HDF5Array S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment Matrix methods utils assertthat: tools HilbertVis: grid lattice GenomicScores: S4Vectors GenomicRanges methods BiocGenerics stats utils XML httr Biobase BiocManager BiocFileCache IRanges Biostrings GenomeInfoDb AnnotationHub rhdf5 DelayedArray HDF5Array R.huge: R.methodsS3 R.oo R.utils LaplacesDemon: parallel grDevices graphics stats utils TargetScore: pracma Matrix TFBSTools: Biobase Biostrings pwalign BiocGenerics BiocParallel BSgenome caTools CNEr DirichletMultinomial GenomeInfoDb GenomicRanges gtools grid IRanges methods DBI RSQLite rtracklayer seqLogo S4Vectors TFMPvalue XML XVector parallel skmeans: slam clue cluster stats utils beachmat.tiledb: methods beachmat tiledb TileDBArray DelayedArray Rcpp assorthead AffymetrixDataTestFiles: scry: stats methods DelayedArray glmpca Matrix SingleCellExperiment SummarizedExperiment BiocSingular pram: methods BiocParallel tools utils data.table GenomicAlignments rtracklayer BiocGenerics GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors ShortRead: BiocGenerics BiocParallel Biostrings Rsamtools GenomicAlignments Biobase S4Vectors IRanges GenomeInfoDb GenomicRanges pwalign hwriter methods lattice latticeExtra XVector Rhtslib MBAmethyl: XINA: mclust plyr alluvial ggplot2 igraph gridExtra tools grDevices graphics utils STRINGdb mCSEA: mCSEAdata Homo.sapiens biomaRt fgsea GenomicFeatures GenomicRanges ggplot2 graphics grDevices Gviz IRanges limma methods parallel S4Vectors stats SummarizedExperiment utils SpaNorm: edgeR ggplot2 Matrix matrixStats methods rlang scran SeuratObject SingleCellExperiment SpatialExperiment stats SummarizedExperiment S4Vectors utils ruv: stats ggplot2 scales gridExtra 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 GWASTools: Biobase graphics stats utils methods gdsfmt DBI RSQLite GWASExactHW DNAcopy survival sandwich lmtest logistf quantsmooth data.table KernSmooth: stats MassArray: methods graphics grDevices stats utils geepack: methods MASS broom magrittr checkmate: backports utils BG2: GA caret memoise Matrix MASS stats ChemmineOB: methods BiocGenerics zlibbioc Rcpp BH conicfit: pracma geigen RnaSeqSampleSize: ggplot2 RnaSeqSampleSizeData biomaRt edgeR heatmap3 matlab KEGGREST methods grDevices graphics stats Rcpp recount ggpubr SummarizedExperiment tidyr dplyr tidyselect utils MSnbase: methods BiocGenerics Biobase mzR S4Vectors ProtGenerics MsCoreUtils PSMatch BiocParallel IRanges plyr vsn grid stats4 affy impute pcaMethods MALDIquant mzID digest lattice ggplot2 scales MASS Rcpp human610quadv1bCrlmm: utils RVS: GENLIB gRain snpStats kinship2 methods stats utils R.utils spatstat.utils: stats graphics grDevices utils methods commonmark: MuData: Matrix S4Vectors rhdf5 methods stats MultiAssayExperiment SingleCellExperiment SummarizedExperiment DelayedArray factoextra: ggplot2 abind cluster dendextend FactoMineR ggpubr grid stats reshape2 ggrepel tidyr crisprViz: crisprBase crisprDesign BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicFeatures GenomicRanges grDevices Gviz IRanges methods S4Vectors txdbmaker IlluminaHumanMethylation450kanno.ilmn12.hg19: minfi metapod: Rcpp lmom: stats graphics arrayQualityMetrics: affy affyPLM beadarray Biobase genefilter graphics grDevices grid gridSVG Hmisc hwriter lattice latticeExtra limma methods RColorBrewer setRNG stats utils vsn XML svglite SBGNview: pathview SBGNview.data Rdpack grDevices methods stats utils xml2 rsvg igraph rmarkdown knitr SummarizedExperiment AnnotationDbi httr KEGGREST bookdown beepr: audio InTAD: methods S4Vectors IRanges GenomicRanges MultiAssayExperiment SummarizedExperiment stats BiocGenerics Biobase rtracklayer parallel graphics mclust qvalue ggplot2 utils ggpubr rcdk: rcdklibs fingerprint rJava methods png iterators itertools AlgDesign: Rvisdiff: edgeR utils BWStest: memoise Rcpp relations: cluster stats slam sets graphics grDevices fedup: openxlsx tibble dplyr data.table ggplot2 ggthemes forcats RColorBrewer RCy3 utils stats ggtreeExtra: ggplot2 utils rlang ggnewscale stats ggtree tidytree cli magrittr qsea: Biostrings graphics gtools methods stats utils HMMcopy rtracklayer BSgenome GenomicRanges Rsamtools IRanges limma GenomeInfoDb BiocGenerics grDevices zoo BiocParallel S4Vectors ellipsis: rlang RNAsense: ggplot2 parallel NBPSeq qvalue SummarizedExperiment stats utils methods rsvd: Matrix OutSplice: AnnotationDbi GenomicRanges GenomicFeatures IRanges org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene S4Vectors norm: stats hgu95av2.db: methods AnnotationDbi org.Hs.eg.db imp4p: Iso stats truncnorm norm missForest missMDA Rcpp rsvg: LungCancerACvsSCCGEO: DLBCL: Biobase graph keggorthology: hgu95av2.db graph AnnotationDbi DBI grDevices methods tools utils ggthemes: ggplot2 graphics grid lifecycle methods purrr scales stringr tibble monocle: methods Matrix Biobase ggplot2 VGAM DDRTree parallel igraph BiocGenerics HSMMSingleCell plyr cluster combinat fastICA grid irlba matrixStats Rtsne MASS reshape2 leidenbase limma tibble dplyr pheatmap stringr proxy slam viridis stats biocViews RANN Rcpp simpleCache: EGAD: gplots Biobase GEOquery limma impute RColorBrewer zoo igraph plyr MASS RCurl methods MetaboSignal: KEGGgraph hpar igraph RCurl KEGGREST EnsDb.Hsapiens.v75 stats graphics utils org.Hs.eg.db biomaRt AnnotationDbi MWASTools mygene aws: awsMethods methods gsl ggfun: cli dplyr ggplot2 grid rlang utils yulab.utils TileDBArray: SparseArray DelayedArray methods tiledb S4Vectors Homo.sapiens: AnnotationDbi methods OrganismDbi GenomicFeatures GO.db org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene R.rsp: methods stats tools utils R.methodsS3 R.oo R.utils R.cache digest sSeq: caTools RColorBrewer microbiome: phyloseq ggplot2 Biostrings compositions dplyr reshape2 Rtsne scales stats tibble tidyr utils vegan bgx: Biobase affy gcrma Rcpp mouse4302cdf: utils AnnotationDbi base64url: backports ashr: Matrix stats graphics Rcpp truncnorm mixsqp SQUAREM etrunct invgamma BgeeDB: topGO tidyr R.utils data.table curl RCurl digest methods stats utils dplyr RSQLite graph Biobase zellkonverter anndata HDF5Array bread SIM: quantreg graphics stats globaltest quantsmooth protolite: Rcpp jsonlite bamsignals: methods BiocGenerics Rcpp IRanges GenomicRanges zlibbioc Rhtslib httr2: cli curl glue lifecycle magrittr openssl R6 rappdirs rlang vctrs withr biodbNcbi: biodb R6 XML chk GetoptLong: rjson GlobalOptions methods crayon 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 ggVennDiagram: ggplot2 dplyr methods tibble aplot venn yulab.utils forcats ggkegg: ggplot2 ggraph XML igraph tidygraph BiocFileCache data.table dplyr magick patchwork shadowtext stringr tibble methods utils stats grDevices gtable DMCFB: SummarizedExperiment methods S4Vectors BiocParallel GenomicRanges IRanges utils stats speedglm MASS data.table splines arm rtracklayer benchmarkme tibble matrixStats fastDummies graphics rCGH: methods stats utils graphics plyr DNAcopy lattice ggplot2 grid shiny limma affy mclust TxDb.Hsapiens.UCSC.hg18.knownGene TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene org.Hs.eg.db GenomicFeatures GenomeInfoDb GenomicRanges AnnotationDbi parallel IRanges grDevices aCGH geometries: Rcpp rebus: rebus.base rebus.datetimes rebus.numbers rebus.unicode spBayes: coda sp magic Formula Matrix seahtrue: dplyr readxl logger tidyxl purrr tidyr lubridate stringr tibble validate rlang glue cli janitor ggplot2 RColorBrewer colorspace forcats ggridges readr scales methylGSA: RobustRankAggreg ggplot2 stringr stats clusterProfiler missMethyl org.Hs.eg.db reactome.db BiocParallel GO.db AnnotationDbi shiny IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylationEPICanno.ilm10b4.hg19 restfulr: methods XML RCurl rjson S4Vectors yaml heatmaply: plotly viridis ggplot2 dendextend magrittr reshape2 scales seriation utils stats grDevices methods colorspace RColorBrewer htmlwidgets webshot assertthat egg gstat: utils stats graphics methods lattice sp zoo sf sftime spacetime stars FNN procoil: kebabs methods stats graphics S4Vectors Biostrings utils graph: methods BiocGenerics stats stats4 utils riboSeqR: methods GenomicRanges abind Rsamtools IRanges S4Vectors baySeq GenomeInfoDb seqLogo bit: FlowSorted.Blood.EPIC: minfi ExperimentHub genefilter nlme quadprog graphics stats utils AnnotationHub SummarizedExperiment S4Vectors repmis: data.table digest httr plyr R.cache plot3D: misc3d stats graphics grDevices methods koRpus: sylly data.table methods Matrix grImport2: methods grDevices grid XML png jpeg base64enc TCGAbiolinksGUI.data: metabinR: methods rJava NBPSeq: splines qvalue scales: cli farver glue labeling lifecycle munsell R6 RColorBrewer rlang viridisLite maSigPro: Biobase graphics grDevices venn mclust stats MASS multicool: methods Rcpp epidecodeR: EnvStats ggplot2 rtracklayer GenomicRanges IRanges rstatix ggpubr methods stats utils dplyr PanViz: tidyr stringr dplyr tibble magrittr futile.logger utils easycsv rentrez igraph RColorBrewer data.table colorspace grDevices rlang methods rebook: utils methods knitr rmarkdown CodeDepends dir.expiry filelock BiocStyle SPsimSeq: stats methods SingleCellExperiment fitdistrplus graphics edgeR Hmisc WGCNA limma mvtnorm phyloseq utils textstem: koRpus.lang.en dplyr hunspell koRpus lexicon quanteda SnowballC stats stringi textclean textshape utils TFMPvalue: Rcpp ReactomeGSA.data: limma edgeR ReactomeGSA Seurat NetSAM: seriation igraph tools WGCNA biomaRt methods AnnotationDbi doParallel foreach survival GO.db R2HTML DBI PMCMRplus: mvtnorm multcompView gmp Rmpfr SuppDists kSamples BWStest MASS stats snakecase: stringr stringi cBioPortalData: AnVIL MultiAssayExperiment BiocBaseUtils BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges methods readr RaggedExperiment RTCGAToolbox S4Vectors SummarizedExperiment stats tibble tidyr TCGAutils utils mbQTL: MatrixEQTL dplyr ggplot2 readxl stringr tidyr metagenomeSeq pheatmap broom graphics stats methods glmSparseNet: biomaRt checkmate dplyr forcats futile.logger ggplot2 glue httr lifecycle methods parallel readr rlang glmnet Matrix MultiAssayExperiment SummarizedExperiment survminer TCGAutils utils RSQLite: bit64 blob DBI memoise methods pkgconfig rlang plogr cpp11 TEQC: methods BiocGenerics IRanges Rsamtools hwriter Biobase quanteda: methods fastmatch jsonlite lifecycle magrittr Matrix Rcpp SnowballC stopwords stringi xml2 yaml miniUI: shiny htmltools utils BaalChIP: GenomicRanges IRanges Rsamtools GenomicAlignments GenomeInfoDb doParallel parallel doBy reshape2 scales coda foreach ggplot2 methods utils graphics stats httpcode: AHMassBank: AnnotationHubData BUSpaRse: AnnotationDbi AnnotationFilter biomaRt BiocGenerics Biostrings BSgenome dplyr ensembldb GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges magrittr Matrix methods plyranges Rcpp S4Vectors stats stringr tibble tidyr utils zeallot RcppArmadillo RcppProgress BH pcalg: stats graphics utils methods abind graph RBGL igraph ggm corpcor robustbase vcd Rcpp bdsmatrix sfsmisc fastICA clue RcppArmadillo BH NetActivity: airway DelayedArray DelayedMatrixStats DESeq2 methods NetActivityData SummarizedExperiment utils RTCGA.miRNASeq: RTCGA ArrayExpress: Biobase oligo limma httr utils jsonlite rlang tools methods sparkline: htmltools htmlwidgets BMA: survival leaps robustbase inline rrcov methods MOMA: circlize cluster ComplexHeatmap dplyr ggplot2 graphics grid grDevices magrittr methods MKmisc MultiAssayExperiment parallel qvalue RColorBrewer readr reshape2 rlang stats stringr tibble tidyr utils shinyFiles: htmltools jsonlite tools shiny fs tibble SplicingGraphs: GenomicFeatures GenomicAlignments Rgraphviz methods utils graphics igraph BiocGenerics S4Vectors BiocParallel IRanges GenomeInfoDb GenomicRanges Rsamtools graph tidyCoverage: SummarizedExperiment S4Vectors IRanges GenomicRanges GenomeInfoDb BiocParallel BiocIO rtracklayer methods tidyr ggplot2 dplyr fansi pillar rlang scales cli purrr vctrs stats ggrepel: ggplot2 grid Rcpp rlang scales withr Rcpi: Biostrings GOSemSim curl doParallel foreach httr2 jsonlite methods rlang stats utils sna: utils statnet.common network PANR: igraph graphics grDevices MASS methods pvclust stats utils RedeR parallel: tools compiler SAVER: glmnet foreach methods iterators doParallel Matrix transport: grDevices graphics methods stats Rcpp data.table RcppEigen shinythemes: shiny stars: abind sf methods parallel classInt rlang units Rcpp: methods utils diffobj: crayon tools methods utils stats esquisse: bslib datamods downlit ggplot2 grDevices htmltools jsonlite phosphoricons rlang rstudioapi scales shiny shinybusy shinyWidgets rematch2: tibble echarts4r: htmlwidgets dplyr purrr countrycode broom shiny scales corrplot htmltools jsonlite rstudioapi kmer: openssl phylogram Rcpp parallelMap: BBmisc checkmate parallel stats utils bayNorm: Rcpp BB foreach iterators doSNOW Matrix parallel MASS locfit fitdistrplus stats methods graphics grDevices SingleCellExperiment SummarizedExperiment BiocParallel utils RcppArmadillo RcppProgress ssrch: methods shiny DT utils pathlinkR: circlize clusterProfiler ComplexHeatmap dplyr fgsea ggforce ggplot2 ggpubr ggraph ggrepel grid igraph purrr sigora stringr tibble tidygraph tidyr vegan visNetwork TVTB: methods utils stats AnnotationFilter BiocGenerics BiocParallel Biostrings ensembldb GenomeInfoDb GenomicRanges GGally ggplot2 Gviz limma IRanges reshape2 Rsamtools S4Vectors SummarizedExperiment VariantAnnotation snm: corpcor lme4 splines LambertW: MASS ggplot2 lamW stats graphics grDevices RColorBrewer reshape2 Rcpp methods bmp: phosphonormalizer: plyr stats graphics matrixStats methods epivizrChart: epivizrData epivizrServer htmltools rjson methods BiocGenerics SIMLR: parallel Matrix stats methods Rcpp pracma RcppAnnoy RSpectra lattice: grid grDevices graphics stats utils keras3: generics reticulate tensorflow tfruns magrittr zeallot fastmap glue cli rlang bcSeq: Rcpp Matrix Biostrings wiggleplotr: dplyr ggplot2 GenomicRanges rtracklayer cowplot assertthat purrr S4Vectors IRanges GenomeInfoDb rmarkdown: bslib evaluate fontawesome htmltools jquerylib jsonlite knitr methods tinytex tools utils xfun yaml Spectra: S4Vectors BiocParallel ProtGenerics methods IRanges MsCoreUtils graphics grDevices stats tools utils fs BiocGenerics MetaboCoreUtils survMisc: survival graphics grDevices stats utils knitr KMsurv ggplot2 data.table zoo grid gridExtra km.ci xtable waffle: ggplot2 RColorBrewer grid gridExtra gtable extrafont curl stringr stats htmlwidgets DT plyr rlang utils TCGAMethylation450k: confintr: boot stats som: trigger: corpcor qtl qvalue methods graphics sva anota: qvalue multtest isobar: Biobase stats methods distr plyr biomaRt ggplot2 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 uwot: Matrix FNN irlba methods Rcpp RcppAnnoy RSpectra dqrng RcppProgress celestial: RANN NISTunits pracma MetMashR: struct dplyr methods httr scales ggthemes ggplot2 utils rlang cowplot stats GAprediction: glmnet stats utils Matrix metabomxtr: methods Biobase optimx Formula plyr multtest BiocParallel ggplot2 sechm: SummarizedExperiment ComplexHeatmap S4Vectors seriation circlize methods randomcoloR stats grid grDevices matrixStats dqrng: Rcpp BH sitmo unifiedWMWqPCR: methods BiocGenerics limma stats graphics stats: utils grDevices graphics readODS: cellranger minty stringi tibble vctrs zip tools cpp11 VegaMC: biomaRt Biobase methods VariantAnnotation: methods BiocGenerics MatrixGenerics GenomeInfoDb GenomicRanges SummarizedExperiment Rsamtools utils DBI Biobase S4Vectors IRanges XVector Biostrings AnnotationDbi rtracklayer BSgenome GenomicFeatures Rhtslib RCASPAR: biodbUniprot: R6 biodb cvar: gbutils Rdpack webdriver: callr base64enc curl debugme httr jsonlite R6 showimage utils withr HMMcopy: data.table TypeInfo: methods RCSL: RcppAnnoy igraph NbClust Rtsne ggplot2 methods pracma umap grDevices graphics stats Rcpp MatrixGenerics SingleCellExperiment dlstats: ggplot2 jsonlite magrittr RColorBrewer scales utils humanCHRLOC: R3CPET: Rcpp methods parallel ggplot2 pheatmap clValid igraph data.table reshape2 Hmisc RCurl BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges ggbio optparse: methods getopt RTCGA.RPPA: RTCGA curl: CytoDx: doParallel dplyr glmnet rpart rpart.plot stats flowCore grDevices graphics utils colorspace: methods graphics grDevices stats TAM: CDM graphics methods Rcpp stats utils RcppArmadillo SQN: mclust nor1mix R.filesets: R.oo digest R.methodsS3 R.utils R.cache stats VisiumIO: TENxIO BiocBaseUtils BiocGenerics BiocIO jsonlite methods S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment lpNet: lpSolve KEGGgraph org.Ce.eg.db: methods AnnotationDbi desc: cli R6 utils sincell: igraph Rcpp entropy scatterplot3d MASS TSP ggplot2 reshape2 fields proxy parallel Rtsne fastICA cluster statmod fitdistrplus: MASS grDevices survival methods stats rlang MPAC: data.table SummarizedExperiment BiocParallel fitdistrplus igraph BiocSingular 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grDevices GenomicRanges IRanges Biostrings MultiMed: cyclocomp: callr crayon desc remotes withr macrophage: sourcetools: quadprog: shinytest: assertthat callr crayon debugme digest htmlwidgets httpuv httr jsonlite parsedate pingr R6 rematch rlang rstudioapi shiny testthat utils webdriver withr ggstar: grid utils ggplot2 scales gridExtra cli instantiate: callr fs rlang utils treekoR: stats utils tidyr dplyr data.table ggiraph ggplot2 hopach ape ggtree patchwork SingleCellExperiment diffcyt edgeR lme4 multcomp ginmappeR: KEGGREST UniProt.ws XML rentrez httr utils memoise cachem jsonlite rvest ggraph: ggplot2 dplyr ggforce grid igraph scales MASS ggrepel utils stats viridis rlang tidygraph graphlayouts withr cli vctrs lifecycle memoise cpp11 decoupleR: BiocParallel broom dplyr magrittr Matrix parallelly purrr rlang stats stringr tibble tidyr tidyselect withr mmand: methods Rcpp msigdb: ExperimentHub utils GSEABase org.Mm.eg.db org.Hs.eg.db AnnotationDbi methods stats AnnotationHub HMM: podkat: methods Rsamtools GenomicRanges Rcpp parallel stats graphics grDevices utils Biobase BiocGenerics Matrix GenomeInfoDb IRanges Biostrings BSgenome Rhtslib ExperimentHub: methods BiocGenerics AnnotationHub BiocFileCache utils S4Vectors BiocManager rappdirs phyloseq: ade4 ape Biobase BiocGenerics biomformat Biostrings cluster data.table foreach ggplot2 igraph methods multtest plyr reshape2 scales vegan StabMap: igraph slam BiocNeighbors Matrix MASS abind SummarizedExperiment methods MatrixGenerics BiocGenerics BiocSingular BiocParallel seqcombo: ggplot2 grid igraph utils yulab.utils GenomicDataCommons: stats httr xml2 jsonlite utils rlang readr GenomicRanges IRanges dplyr rappdirs tibble tidyr ReactomeGSA: Biobase BiocSingular dplyr ggplot2 gplots httr igraph jsonlite methods progress RColorBrewer SummarizedExperiment tidyr Structstrings: S4Vectors IRanges Biostrings methods BiocGenerics XVector stringr stringi crayon grDevices hms: lifecycle methods pkgconfig rlang vctrs 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S4Vectors stats graphics grDevices BiocGenerics GenomeInfoDb IRanges BiocParallel qvalue TxDb.Hsapiens.UCSC.hg38.knownGene org.Hs.eg.db utils DELocal: DESeq2 dplyr reshape2 limma SummarizedExperiment ggplot2 matrixStats stats DeepTarget: fgsea ggplot2 stringr ggpubr BiocParallel pROC stats grDevices graphics depmap readr dplyr seqPattern: methods Biostrings GenomicRanges IRanges KernSmooth plotrix fmsb: DelayedMatrixStats: MatrixGenerics DelayedArray methods sparseMatrixStats Matrix S4Vectors IRanges SparseArray ncGTW: methods BiocParallel xcms Rcpp grDevices graphics stats fmrs: methods survival stats BufferedMatrixMethods: BufferedMatrix methods rebus.datetimes: rebus.base praznik: benchmarkmeData: dplyr graphics tibble utils showtextdb: sysfonts utils graper: Matrix Rcpp stats ggplot2 methods cowplot matrixStats RcppArmadillo BH cellmigRation: methods foreach tiff graphics stats utils reshape2 parallel doParallel grDevices matrixStats FME SpatialTools sp vioplot FactoMineR Hmisc 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foreach doParallel methods tidyr dplyr ConsRank rgoslin: Rcpp dplyr imcdatasets: SingleCellExperiment SpatialExperiment cytomapper methods utils ExperimentHub S4Vectors DelayedArray HDF5Array broadSeq: dplyr ggpubr SummarizedExperiment BiocStyle DELocal EBSeq DESeq2 NOISeq forcats genefilter ggplot2 ggplotify plyr clusterProfiler pheatmap sechm stringr purrr edgeR StanHeaders: RcppParallel RcppEigen BSgenome.Rnorvegicus.UCSC.rn5.masked: BSgenome BSgenome.Rnorvegicus.UCSC.rn5 rtracklayer: methods GenomicRanges XML BiocGenerics S4Vectors IRanges XVector GenomeInfoDb Biostrings curl httr Rsamtools GenomicAlignments BiocIO tools restfulr flowPloidyData: GraphAT: graph methods MCMCpack stats rclipboard: shiny bslib findpython: MPRAnalyze: BiocParallel methods progress stats SummarizedExperiment multcomp: stats graphics mvtnorm survival TH.data sandwich codetools geneLenDataBase: utils rtracklayer GenomicFeatures txdbmaker illuminaHumanv1.db: methods AnnotationDbi org.Hs.eg.db timecoursedata: SummarizedExperiment fftwtools: hwriter: biscuiteer: biscuiteerData bsseq readr qualV Matrix impute HDF5Array S4Vectors Rsamtools data.table Biobase GenomicRanges IRanges BiocGenerics VariantAnnotation DelayedMatrixStats SummarizedExperiment GenomeInfoDb Mus.musculus Homo.sapiens matrixStats rtracklayer QDNAseq dmrseq methods utils R.utils gtools BiocParallel rafalib: RColorBrewer frmaTools: affy Biobase DBI methods preprocessCore stats utils umap: Matrix methods openssl reticulate Rcpp RSpectra stats SMVar: msdata: RTNsurvival: RTN RTNduals methods survival RColorBrewer grDevices graphics stats utils scales data.table egg ggplot2 pheatmap dunn.test ARRmData: randomForestSRC: parallel data.tree DiagrammeR sosta: terra sf smoothr spatstat.explore spatstat.geom SpatialExperiment dplyr ggplot2 patchwork SummarizedExperiment stats rlang parallel plsVarSel: pls grDevices graphics genalg mvtnorm bdsmatrix MASS progress parallel stats praznik markdown: utils commonmark xfun 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matrixStats ibh: simpIntLists GeneRegionScan: methods Biobase Biostrings S4Vectors affxparser RColorBrewer pingr: processx utils ChemoSpecUtils: data.table ggplot2 ggrepel plotly magrittr minqa: Rcpp MEAT: impute dynamicTreeCut glmnet grDevices graphics stats utils stringr tibble RPMM minfi dplyr SummarizedExperiment wateRmelon ica: propagate: MASS tmvtnorm Rcpp ff minpack.lm STATegRa: Biobase gridExtra ggplot2 methods stats grid MASS calibrate gplots edgeR limma foreach affy timescape: htmlwidgets jsonlite stringr dplyr gtools ttgsea: keras tm text2vec tokenizers textstem stopwords data.table purrr DiagrammeR stats bookdown: htmltools knitr rmarkdown jquerylib xfun tinytex yaml reader: utils NCmisc grDevices graphics stats methods HilbertCurve: grid methods utils png grDevices circlize IRanges GenomicRanges polylabelr Rcpp SharedObject: Rcpp methods stats BiocGenerics BH gridBase: graphics grid ParamHelpers: backports BBmisc checkmate fastmatch methods abind: methods utils phylobase: 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Matrix S4Vectors methods utils pkgconfig tibble dplyr tidyr ggplot2 plotly rlang purrr stringr vctrs tidyselect pillar cli fansi lifecycle magick tidygate shiny lintr: backports codetools cyclocomp digest glue knitr rex stats utils xml2 xmlparsedata fontawesome: rlang htmltools Rcapture: stats graphics utils clusterSeq: methods BiocParallel baySeq graphics stats utils BiocGenerics BREW3R.r: GenomicRanges methods rlang S4Vectors utils ggforce: ggplot2 Rcpp grid scales MASS tweenr gtable rlang polyclip stats grDevices tidyselect withr utils lifecycle cli vctrs systemfonts RcppEigen rgsepd: DESeq2 goseq gplots biomaRt org.Hs.eg.db GO.db SummarizedExperiment AnnotationDbi ggfortify: methods ggplot2 dplyr tidyr gridExtra grid scales stringr tibble tidygate: utils graphics lifecycle scales magrittr tibble dplyr purrr rlang tidyr viridis grDevices RColorBrewer stringr shiny plotly ggplot2 mosaicCore: stats dplyr rlang tidyr MASS bigassertr: cosmiq: Rcpp pracma xcms MassSpecWavelet faahKO 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GenomicAlignments GenomicRanges IRanges Biostrings DNAcopy Rsamtools parallel stringr BoolNet: igraph XML diffcyt: flowCore FlowSOM SummarizedExperiment S4Vectors limma edgeR lme4 multcomp dplyr tidyr reshape2 magrittr stats methods utils grDevices graphics ComplexHeatmap circlize grid wrswoR: logging Rcpp metafor: methods Matrix metadat numDeriv stats utils graphics grDevices nlme mathjaxr pbapply digest EnsDb.Hsapiens.v75: ensembldb AGDEX: Biobase GSEABase stats nnSVG: SpatialExperiment SingleCellExperiment SummarizedExperiment BRISC BiocParallel Matrix matrixStats stats methods RcppSpdlog: Rcpp EnsDb.Hsapiens.v79: ensembldb shinyalert: htmltools shiny uuid future: digest globals listenv parallel parallelly utils PtH2O2lipids: xcms CAMERA LOBSTAHS methods utils rappdirs: plotGrouper: ggplot2 dplyr tidyr tibble stringr readr readxl scales stats grid gridExtra egg gtable ggpubr shiny shinythemes colourpicker magrittr Hmisc rlang Signac: methods GenomeInfoDb GenomicRanges IRanges Matrix 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rlang httr openxlsx htmltools reshape2 reactable msigdbr kableExtra rmarkdown igraph visNetwork shiny BiocStyle OMICsPCA: OMICsPCAdata HelloRanges fpc stats MultiAssayExperiment pdftools methods grDevices utils clValid NbClust cowplot rmarkdown kableExtra rtracklayer IRanges GenomeInfoDb reshape2 ggplot2 factoextra rgl corrplot MASS graphics FactoMineR PerformanceAnalytics tidyr data.table cluster magick tfprobability: tensorflow reticulate keras magrittr categoryCompare: Biobase BiocGenerics AnnotationDbi hwriter GSEABase Category GOstats annotate colorspace graph RCy3 methods grDevices utils MsBackendMetaboLights: Spectra curl ProtGenerics BiocFileCache S4Vectors methods tidygraph: cli dplyr igraph lifecycle magrittr pillar R6 rlang stats tibble tidyr tools utils cpp11 BSgenome.Btaurus.UCSC.bosTau6.masked: BSgenome BSgenome.Btaurus.UCSC.bosTau6 evmix: stats graphics MASS splines gsl SparseM grDevices tidytidbits: utils stats grDevices methods rlang dplyr forcats grid purrr stringr 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ontologyIndex datasets graphics stats utils knitr SummarizedExperiment S4Vectors rols GSEAlm: Biobase UniProt.ws: AnnotationDbi AnVILBase BiocFileCache BiocBaseUtils BiocGenerics httr2 jsonlite methods progress rjsoncons utils receptLoss: dplyr ggplot2 magrittr tidyr SummarizedExperiment modeest: fBasics stable stabledist stats statip palmerpenguins: MOGAMUN: stats utils RCy3 stringr graphics grDevices RUnit BiocParallel igraph DiceKriging: methods xcms: BiocParallel MSnbase mzR methods Biobase BiocGenerics ProtGenerics lattice MassSpecWavelet S4Vectors IRanges SummarizedExperiment MsCoreUtils MsFeatures MsExperiment Spectra progress RColorBrewer MetaboCoreUtils RTCGA.methylation: RTCGA mariner: methods S4Vectors BiocGenerics BiocManager GenomicRanges InteractionSet data.table stats rlang glue assertthat plyranges magrittr dbscan purrr progress GenomeInfoDb strawr DelayedArray HDF5Array abind BiocParallel IRanges SummarizedExperiment rhdf5 plotgardener RColorBrewer colourvalues utils 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stringr ggplot2 graphics grDevices calibrate corrgram gridExtra DT shiny shinydashboard readxl prodlim matrixStats BSgenome.Rnorvegicus.UCSC.rn5: BSgenome BSgenome.Rnorvegicus.UCSC.rn6: BSgenome mlr: ParamHelpers backports BBmisc checkmate data.table ggplot2 methods parallelMap stats stringi survival utils XML breastCancerVDX: ggExtra: colourpicker ggplot2 grDevices grid gtable miniUI scales shiny shinyjs utils R6 BSgenome.Rnorvegicus.UCSC.rn7: BSgenome berryFunctions: grDevices graphics stats utils abind ELMER: ELMER.data GenomicRanges ggplot2 reshape grid grDevices graphics methods parallel stats utils IRanges GenomeInfoDb S4Vectors GenomicFeatures TCGAbiolinks plyr Matrix dplyr Gviz ComplexHeatmap circlize MultiAssayExperiment SummarizedExperiment biomaRt doParallel downloader ggrepel lattice magrittr readr scales rvest xml2 plotly gridExtra rmarkdown stringr tibble tidyr progress purrr reshape2 ggpubr rtracklayer DelayedArray R.matlab: methods utils R.methodsS3 R.oo R.utils 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stats Mfuzz: Biobase e1071 tcltk tkWidgets zCompositions: methods MASS NADA truncnorm tfautograph: reticulate backports MafDb.gnomADex.r2.1.hs37d5: GenomicScores utils S4Vectors IRanges GenomicRanges GenomeInfoDb BSgenome roar: methods BiocGenerics S4Vectors IRanges GenomicRanges SummarizedExperiment GenomicAlignments rtracklayer GenomeInfoDb org.Mm.eg.db: methods AnnotationDbi veloviz: Rcpp Matrix igraph mgcv RSpectra grDevices graphics stats fgsea: Rcpp data.table BiocParallel stats ggplot2 cowplot grid fastmatch Matrix scales utils BH SPIA: graphics KEGGgraph NCIgraph: graph KEGGgraph methods RBGL RCy3 R.oo matrixStats: multistateQTL: QTLExperiment SummarizedExperiment ComplexHeatmap data.table collapse methods S4Vectors grid dplyr tidyr matrixStats stats fitdistrplus viridis ggplot2 circlize mashr grDevices MetNet: S4Vectors SummarizedExperiment bnlearn BiocParallel corpcor dplyr ggplot2 GeneNet GENIE3 methods parmigene psych rlang stabs stats tibble tidyr visiumStitched: 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Rcpp S4Vectors SingleCellExperiment stats SummarizedExperiment utils mitch: stats grDevices graphics utils MASS plyr reshape2 parallel GGally grid gridExtra knitr rmarkdown ggplot2 gplots beeswarm echarts4r kableExtra maCorrPlot: lattice graphics grDevices stats CIMICE: dplyr ggplot2 glue tidyr igraph networkD3 visNetwork ggcorrplot purrr ggraph stats utils maftools assertthat tidygraph expm Matrix robslopes: Rcpp RcppArmadillo MatrixCorrelation: Rcpp plotrix pracma progress RSpectra RcppArmadillo crochet: methods spaSim: ggplot2 methods stats dplyr spatstat.geom spatstat.random SpatialExperiment SummarizedExperiment RANN stats4: graphics methods stats covr: methods digest stats utils jsonlite rex httr crayon withr yaml countrycode: illuminaHumanv4.db: methods AnnotationDbi org.Hs.eg.db ggsci: ggplot2 grDevices scales compareGroups: survival tools HardyWeinberg rmarkdown knitr kableExtra methods chron stats writexl flextable officer PMCMRplus SCArray.sat: methods SCArray SeuratObject Seurat S4Vectors utils stats BiocGenerics BiocParallel gdsfmt DelayedArray BiocSingular SummarizedExperiment Matrix SCnorm: SingleCellExperiment SummarizedExperiment stats methods graphics grDevices parallel quantreg cluster moments data.table BiocParallel S4Vectors ggplot2 forcats BiocGenerics spdl: RcppSpdlog mlr3learners: mlr3 checkmate data.table mlr3misc paradox R6 splots: grid RColorBrewer DiffBind: GenomicRanges SummarizedExperiment RColorBrewer amap gplots grDevices limma GenomicAlignments locfit stats utils IRanges lattice systemPipeR tools Rcpp dplyr ggplot2 BiocParallel parallel S4Vectors Rsamtools DESeq2 methods graphics ggrepel apeglm ashr GreyListChIP Rhtslib PANTHER.db: AnnotationDbi AnnotationHub utils methods RSQLite BiocFileCache methrix: data.table SummarizedExperiment rtracklayer DelayedArray HDF5Array BSgenome DelayedMatrixStats parallel methods ggplot2 S4Vectors matrixStats graphics stats utils GenomicRanges IRanges estimability: stats cogeqc: utils graphics stats methods reshape2 ggplot2 scales ggtree patchwork igraph rlang ggbeeswarm jsonlite Biostrings DelayedTensor: methods utils S4Arrays SparseArray DelayedArray HDF5Array BiocSingular rTensor DelayedRandomArray irlba Matrix einsum BlandAltmanLeh: tkrplot: grDevices tcltk recount3: SummarizedExperiment BiocFileCache methods rtracklayer S4Vectors utils httr data.table R.utils Matrix GenomicRanges sessioninfo tools famat: KEGGREST mgcv stats BiasedUrn dplyr gprofiler2 rWikiPathways reactome.db stringr GO.db ontologyIndex tidyr shiny shinydashboard shinyBS plotly magrittr DT clusterProfiler org.Hs.eg.db hopach: cluster Biobase methods graphics grDevices stats utils BiocGenerics roastgsa: parallel grDevices graphics utils stats methods grid RColorBrewer gplots ggplot2 limma Biobase RUVnormalizeData: Biobase pkgbuild: callr cli desc processx R6 docopt: methods networkD3: htmlwidgets igraph magrittr BEDMatrix: methods crochet SNAGEEdata: etrunct: EpiDISH: MASS e1071 quadprog parallel stats matrixStats stringr locfdr Matrix oncomix: ggplot2 ggrepel RColorBrewer mclust stats SummarizedExperiment PureCN: DNAcopy VariantAnnotation GenomicRanges IRanges RColorBrewer S4Vectors data.table grDevices graphics stats utils SummarizedExperiment GenomeInfoDb GenomicFeatures Rsamtools Biobase Biostrings BiocGenerics rtracklayer ggplot2 gridExtra futile.logger VGAM tools methods mclust rhdf5 Matrix BiocVersion: styler: cli magrittr purrr R.cache rlang rprojroot tools vctrs withr SplineDV: plotly dplyr scuttle methods Biobase BiocGenerics S4Vectors sparseMatrixStats SingleCellExperiment SummarizedExperiment Matrix utils ggnetwork: ggplot2 ggrepel network igraph sna utils DGEobj.utils: assertthat DGEobj dplyr methods stats stringr TitanCNA: BiocGenerics IRanges GenomicRanges VariantAnnotation foreach GenomeInfoDb data.table dplyr RcisTarget: AUCell BiocGenerics data.table graphics GenomeInfoDb GenomicRanges arrow dplyr tibble GSEABase methods R.utils stats SummarizedExperiment S4Vectors utils zoo numDeriv: OLIN: methods locfit marray graphics grDevices limma stats RMassBankData: RankProd: stats methods Rmpfr gmp graphics mzR: Rcpp methods utils Biobase BiocGenerics ProtGenerics ncdf4 Rhdf5lib igraph: methods cli graphics grDevices lifecycle magrittr Matrix pkgconfig rlang stats utils vctrs cpp11 flowPloidy: flowCore car caTools knitr rmarkdown minpack.lm shiny methods graphics stats utils spatialHeatmap: data.table dplyr edgeR genefilter ggplot2 grImport grid gridExtra igraph methods Matrix rsvg shiny grDevices graphics ggplotify parallel reshape2 stats SummarizedExperiment SingleCellExperiment shinydashboard S4Vectors spsComps tibble utils xml2 flexmix: lattice graphics grid grDevices methods modeltools nnet stats stats4 utils HDTD: stats Rcpp RcppArmadillo roxygen2: brew cli commonmark desc knitr methods pkgload purrr R6 rlang stringi stringr utils withr xml2 cpp11 ramwas: methods filematrix graphics stats utils digest glmnet KernSmooth grDevices GenomicAlignments Rsamtools parallel biomaRt Biostrings BiocGenerics RNeXML: ape methods XML plyr reshape2 httr uuid dplyr tidyr stringr stringi xml2 rlang easylift: GenomicRanges BiocFileCache rtracklayer GenomeInfoDb R.utils tools methods bdsmatrix: methods BSgenome.Ecoli.NCBI.20080805: BSgenome statebins: ggplot2 scales grid tmvtnorm: mvtnorm utils Matrix stats4 gmm stats methods Rtsne: Rcpp stats erma: methods Homo.sapiens GenomicFiles rtracklayer S4Vectors BiocGenerics GenomicRanges SummarizedExperiment ggplot2 GenomeInfoDb Biobase shiny BiocParallel IRanges AnnotationDbi TENxPBMCData: SingleCellExperiment HDF5Array AnnotationHub ExperimentHub CNVrd2: methods VariantAnnotation parallel rjags ggplot2 gridExtra DNAcopy IRanges Rsamtools DEoptim: parallel methods compEpiTools: methods topGO GenomicRanges AnnotationDbi BiocGenerics Biostrings Rsamtools parallel grDevices gplots IRanges GenomicFeatures XVector methylPipe GO.db S4Vectors GenomeInfoDb AlpsNMR: utils generics graphics stats grDevices cli magrittr dplyr signal rlang scales stringr tibble tidyr tidyselect readxl purrr glue reshape2 mixOmics matrixStats fs rmarkdown speaq htmltools pcaPP ggplot2 baseline vctrs BiocParallel cellscape: dplyr gtools htmlwidgets jsonlite reshape2 stringr aplot: ggfun ggplot2 ggplotify patchwork magrittr methods utils easyPubMed: utils scmap: Biobase SingleCellExperiment SummarizedExperiment BiocGenerics S4Vectors dplyr reshape2 matrixStats proxy utils googleVis ggplot2 methods stats e1071 randomForest Rcpp RcppArmadillo spiky: Rsamtools GenomicRanges stats scales bamlss methods tools IRanges Biostrings GenomicAlignments BlandAltmanLeh GenomeInfoDb BSgenome S4Vectors graphics ggplot2 utils DriverNet: methods ProteoDisco: BiocGenerics BiocParallel Biostrings checkmate cleaver dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges methods ParallelLogger plyr rlang S4Vectors tibble tidyr VariantAnnotation XVector diffHic: GenomicRanges InteractionSet SummarizedExperiment Rsamtools Rhtslib Biostrings BSgenome rhdf5 edgeR limma csaw locfit methods IRanges S4Vectors GenomeInfoDb BiocGenerics grDevices graphics stats utils Rcpp rtracklayer decontam: methods ggplot2 reshape2 stats cbpManager: shiny shinydashboard utils DT htmltools vroom plyr dplyr magrittr jsonlite rapportools basilisk reticulate shinyBS shinycssloaders rintrojs rlang markdown tidySummarizedExperiment: SummarizedExperiment ttservice dplyr tibble magrittr tidyr ggplot2 rlang purrr lifecycle methods utils S4Vectors tidyselect ellipsis vctrs pillar stringr cli fansi stats pkgconfig Maaslin2: robustbase biglm pcaPP edgeR metagenomeSeq pbapply car dplyr vegan chemometrics ggplot2 pheatmap logging data.table lmerTest hash optparse grDevices stats utils glmmTMB MASS cplm pscl lme4 tibble PairedData: methods graphics MASS gld mvtnorm lattice ggplot2 plyranges: BiocGenerics IRanges GenomicRanges methods dplyr rlang magrittr tidyselect rtracklayer GenomicAlignments GenomeInfoDb Rsamtools S4Vectors utils mist: BiocParallel MCMCpack Matrix S4Vectors methods rtracklayer car mvtnorm SummarizedExperiment SingleCellExperiment BiocGenerics stats rlang evaluomeR: SummarizedExperiment MultiAssayExperiment cluster fpc randomForest flexmix RSKC sparcl corrplot grDevices graphics reshape2 ggplot2 ggdendro plotrix stats matrixStats Rdpack MASS class prabclus mclust kableExtra dplyr dendextend CBNplot: ggplot2 magrittr graphite ggraph igraph bnlearn patchwork org.Hs.eg.db clusterProfiler utils enrichplot reshape2 ggforce dplyr tidyr stringr depmap ExperimentHub Rmpfr graphlayouts BiocFileCache ggdist purrr pvclust stats rlang biomvRCNS: IRanges GenomicRanges Gviz methods mvtnorm timeOmics: mixOmics dplyr tidyr tibble purrr magrittr ggplot2 stringr ggrepel lmtest plyr checkmate cplm: coda Matrix splines methods biglm ggplot2 minqa nlme reshape2 statmod stats stats4 tweedie VCFArray: methods BiocGenerics DelayedArray tools GenomicRanges VariantAnnotation GenomicFiles S4Vectors Rsamtools GEOquery: methods Biobase readr xml2 dplyr data.table tidyr magrittr limma curl rentrez R.utils stringr SummarizedExperiment S4Vectors rvest httr2 planet: methods tibble magrittr dplyr AgiMicroRna: methods Biobase limma affy preprocessCore affycoretools sftime: sf methods timeDate: methods graphics utils stats bigmemory: bigmemory.sri methods utils Rcpp uuid BH pd.mapping50k.xba240: Biostrings methods RSQLite oligoClasses oligo DBI IRanges S4Vectors DRIMSeq: utils stats MASS GenomicRanges IRanges S4Vectors BiocGenerics methods BiocParallel limma edgeR ggplot2 reshape2 martini: igraph Matrix memoise methods Rcpp snpStats stats utils RcppEigen hierinf: fmsb glmnet methods parallel stats lambda.r: formatR Rook: utils tools methods brew ggdist: ggplot2 rlang cli scales grid tibble vctrs withr distributional numDeriv glue quadprog gtable Rcpp ALLMLL: affy profmem: utils regionalpcs: dplyr PCAtools tibble GenomicRanges kableExtra: knitr magrittr stringr xml2 rmarkdown scales viridisLite stats grDevices htmltools rstudioapi tools digest graphics svglite tfruns: utils jsonlite base64enc yaml config magrittr whisker tidyselect rlang rstudioapi reticulate bigmemory.sri: methods systemPipeRdata: methods Biostrings BiocGenerics jsonlite remotes RcppHMM: Rcpp RcppArmadillo NLP: utils RedeR: methods scales igraph goftest: stats spatialSimGP: SpatialExperiment MASS SummarizedExperiment PCHiCdata: Chicago ggcyto: methods ggplot2 flowCore ncdfFlow flowWorkspace plyr scales hexbin data.table RColorBrewer gridExtra rlang geneAttribution: utils GenomicRanges org.Hs.eg.db BiocGenerics GenomeInfoDb GenomicFeatures IRanges rtracklayer NMF: methods utils registry rngtools cluster graphics stats stringr digest grid grDevices gridBase colorspace RColorBrewer foreach doParallel ggplot2 reshape2 Biobase codetools BiocManager ggbio: methods BiocGenerics ggplot2 grid grDevices graphics stats utils gridExtra scales reshape2 gtable Hmisc biovizBase Biobase S4Vectors IRanges GenomeInfoDb GenomicRanges SummarizedExperiment Biostrings Rsamtools GenomicAlignments BSgenome VariantAnnotation rtracklayer GenomicFeatures OrganismDbi GGally ensembldb AnnotationDbi AnnotationFilter rlang DEGreport: utils methods Biobase BiocGenerics broom circlize ComplexHeatmap cowplot ConsensusClusterPlus cluster dendextend DESeq2 dplyr edgeR ggplot2 ggdendro grid ggrepel grDevices knitr logging magrittr psych RColorBrewer reshape rlang scales stats stringr stringi S4Vectors SummarizedExperiment tidyr tibble NMI: BrowserViz: jsonlite httpuv methods BiocGenerics ranger: Rcpp Matrix RcppEigen emmeans: estimability graphics methods numDeriv stats utils mvtnorm RTCGA: XML RCurl assertthat stringi rvest data.table xml2 dplyr purrr survival survminer ggplot2 ggthemes viridis knitr scales rmarkdown htmltools GOpro: AnnotationDbi dendextend doParallel foreach parallel org.Hs.eg.db GO.db Rcpp stats graphics MultiAssayExperiment IRanges S4Vectors BH MetaboAnnotation: BiocGenerics MsCoreUtils MetaboCoreUtils ProtGenerics methods S4Vectors Spectra BiocParallel SummarizedExperiment QFeatures AnnotationHub graphics CompoundDb supraHex: hexbin ape MASS grDevices graphics stats readr tibble tidyr dplyr stringr purrr magrittr igraph methods diptest: graphics stats corral: ggplot2 ggthemes grDevices gridExtra irlba Matrix methods MultiAssayExperiment pals reshape2 SingleCellExperiment SummarizedExperiment transport pdfCluster: geometry methods enviPat: vbmp: vioplot: sm zoo cpp11: rstudioapi: cowplot: ggplot2 grid gtable grDevices methods rlang scales lmodel2: BCRANK: methods Biostrings reportr: ore import: rjsoncons: cli tibble cpp11 seqsetvis: ggplot2 cowplot data.table eulerr GenomeInfoDb GenomicAlignments GenomicRanges ggplotify grDevices grid IRanges limma methods pbapply pbmcapply png RColorBrewer Rsamtools rtracklayer S4Vectors scales stats UpSetR billboarder: htmlwidgets htmltools magrittr jsonlite ggplot2 scales shiny rlang plyr: Rcpp basilisk.utils: utils methods tools dir.expiry scMET: methods Rcpp RcppParallel rstan rstantools VGAM data.table MASS logitnorm ggplot2 matrixStats assertthat viridis coda BiocStyle cowplot stats SummarizedExperiment SingleCellExperiment Matrix dplyr S4Vectors BH RcppEigen StanHeaders systemPipeShiny: shiny spsUtil spsComps drawer DT assertthat bsplus crayon dplyr ggplot2 htmltools glue magrittr methods plotly rlang rstudioapi shinyAce shinyFiles shinyWidgets shinydashboard shinydashboardPlus shinyjqui shinyjs shinytoastr stringr stats styler tibble utils vroom yaml R6 RSQLite openssl ABarray: Biobase graphics grDevices methods multtest stats tcltk utils scDataviz: S4Vectors SingleCellExperiment ggplot2 ggrepel flowCore umap Seurat reshape2 scales RColorBrewer corrplot stats grDevices graphics utils MASS matrixStats methods scanMiRApp: scanMiR AnnotationDbi AnnotationFilter AnnotationHub BiocParallel Biostrings data.table digest DT ensembldb fst GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 htmlwidgets IRanges Matrix methods plotly rintrojs rtracklayer S4Vectors scanMiRData shiny shinycssloaders shinydashboard shinyjqui stats utils txdbmaker waiter DeMAND: KernSmooth methods recount: SummarizedExperiment BiocParallel derfinder downloader GEOquery GenomeInfoDb GenomicRanges IRanges methods RCurl rentrez rtracklayer S4Vectors stats utils sSNAPPY: ggplot2 dplyr magrittr rlang stats graphite tibble ggraph igraph reshape2 org.Hs.eg.db SummarizedExperiment edgeR methods ggforce pheatmap utils stringr gtools tidyr singleCellTK: SummarizedExperiment SingleCellExperiment DelayedArray Biobase ape anndata AnnotationHub batchelor BiocParallel celldex colourpicker colorspace cowplot cluster ComplexHeatmap data.table DelayedMatrixStats DESeq2 dplyr DT ExperimentHub ensembldb fields ggplot2 ggplotify ggrepel ggtree gridExtra grid GSVA GSVAdata igraph KernSmooth limma MAST Matrix matrixStats methods msigdbr multtest plotly plyr ROCR Rtsne S4Vectors scater scMerge scran Seurat shiny shinyjs SingleR stringr SoupX sva reshape2 shinyalert circlize enrichR celda shinycssloaders DropletUtils scds reticulate tools tximport tidyr eds withr GSEABase R.utils zinbwave scRNAseq TENxPBMCData yaml rmarkdown magrittr scDblFinder metap VAM tibble rlang TSCAN TrajectoryUtils scuttle utils stats zellkonverter ChIPQC: ggplot2 DiffBind GenomicRanges BiocParallel BiocGenerics S4Vectors IRanges Rsamtools GenomicAlignments chipseq gtools methods reshape2 Nozzle.R1 Biobase grDevices stats utils GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg18.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene TxDb.Mmusculus.UCSC.mm9.knownGene TxDb.Rnorvegicus.UCSC.rn4.ensGene TxDb.Celegans.UCSC.ce6.ensGene TxDb.Dmelanogaster.UCSC.dm3.ensGene TDbasedUFEadv: TDbasedUFE Biobase GenomicRanges utils rTensor methods graphics RTCGA stats enrichplot DOSE STRINGdb enrichR hash shiny org.Bt.eg.db: methods AnnotationDbi roll: Rcpp RcppParallel RcppArmadillo RefManageR: xml2 jsonlite utils plyr tools httr lubridate stringr methods bibtex rphylopic: ggplot2 jsonlite grid graphics png grImport2 rsvg httr curl methods lifecycle pbapply knitr scales diffGeneAnalysis: graphics grDevices minpack.lm stats utils MICSQTL: SummarizedExperiment stats TCA nnls purrr TOAST magrittr BiocParallel ggplot2 ggpubr ggridges glue S4Vectors dirmult rols: methods httr2 jsonlite utils Biobase BiocGenerics hgu133atagprobe: AnnotationDbi TCseq: edgeR BiocGenerics reshape2 GenomicRanges IRanges SummarizedExperiment GenomicAlignments Rsamtools e1071 cluster ggplot2 grid grDevices stats utils methods locfit tomoda: methods stats grDevices reshape2 Rtsne umap RColorBrewer ggplot2 ggrepel SummarizedExperiment RColorBrewer: bigstatsr: bigassertr bigparallelr cowplot foreach ggplot2 graphics methods ps Rcpp rmio RSpectra stats tibble utils RcppArmadillo mitml: pan jomo haven grDevices graphics stats methods utils geneXtendeR: rtracklayer GO.db data.table dplyr graphics networkD3 RColorBrewer SnowballC tm utils wordcloud AnnotationDbi BiocStyle org.Rn.eg.db boot: graphics stats Harman: Rcpp graphics stats Ckmeans.1d.dp parallel methods matrixStats immunotation: stringr ontologyIndex curl ggplot2 readr rvest tidyr xml2 maps rlang distillery: tcltk: utils Damsel: AnnotationDbi Biostrings ComplexHeatmap dplyr edgeR GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 goseq magrittr patchwork plyranges reshape2 rlang Rsamtools Rsubread stats stringr tidyr utils TREG: SummarizedExperiment Matrix purrr rafalib GWASdata: GWASTools ggside: ggplot2 grid gtable rlang scales cli glue stats tibble vctrs BSgenome.Drerio.UCSC.danRer7: BSgenome GOfuncR: vioplot Rcpp mapplots gtools GenomicRanges IRanges AnnotationDbi utils grDevices graphics stats ddPCRclust: plotrix clue parallel ggplot2 openxlsx R.utils flowCore flowDensity SamSPECTRAL flowPeaks omicplotR: ALDEx2 compositions DT grDevices knitr jsonlite matrixStats rmarkdown shiny stats vegan zCompositions cvAUC: ROCR data.table PrInCE: purrr dplyr tidyr forecast progress Hmisc naivebayes robustbase ranger LiblineaR speedglm tester magrittr Biobase MSnbase stats utils methods Rdpack epialleleR: stats methods utils data.table BiocGenerics GenomicRanges Rcpp BH Rhtslib pairedGSEA: DESeq2 DEXSeq limma fgsea sva SummarizedExperiment S4Vectors BiocParallel ggplot2 aggregation stats utils methods mhsmm: mvtnorm methods msImpute: softImpute methods stats graphics pdist reticulate scran data.table FNN matrixStats limma mvtnorm tidyr dplyr PRROC: OCplus: multtest graphics grDevices stats interp ordinal: stats methods ucminf MASS Matrix numDeriv nlme readJDX: stringr CellMixS: kSamples BiocNeighbors ggplot2 scater viridis cowplot SummarizedExperiment SingleCellExperiment tidyr magrittr dplyr ggridges stats purrr methods BiocParallel BiocGenerics minfiData: minfi IlluminaHumanMethylation450kmanifest IlluminaHumanMethylation450kanno.ilmn12.hg19 panelcn.mops: cn.mops methods utils stats graphics GenomicRanges Rsamtools IRanges S4Vectors GenomeInfoDb grDevices survey: grid methods Matrix survival stats graphics splines lattice minqa numDeriv mitools Rcpp RcppArmadillo multiscan: Biobase utils lpSolve: R2jags: rjags abind coda graphics grDevices methods R2WinBUGS parallel stats stringr utils Seurat: methods SeuratObject cluster cowplot fastDummies fitdistrplus future future.apply generics ggplot2 ggrepel ggridges graphics grDevices grid httr ica igraph irlba jsonlite KernSmooth leidenbase lifecycle lmtest MASS Matrix matrixStats miniUI patchwork pbapply plotly png progressr RANN RColorBrewer Rcpp RcppAnnoy RcppHNSW reticulate rlang ROCR RSpectra Rtsne scales scattermore sctransform shiny spatstat.explore spatstat.geom stats tibble tools utils uwot RcppEigen RcppProgress ORFhunteR: Biostrings rtracklayer Peptides Rcpp BSgenome.Hsapiens.UCSC.hg38 data.table stringr randomForest xfun stats utils parallel graphics randomForest: stats ribor: dplyr ggplot2 hash methods rhdf5 rlang stats S4Vectors tidyr tools yaml netboost: Rcpp RcppParallel parallel grDevices graphics stats utils dynamicTreeCut WGCNA impute colorspace methods BiocStyle R.utils CGHregions: methods Biobase CGHbase AnnotationFilter: utils methods GenomicRanges lazyeval HEEBOdata: methylclock: methylclockData devtools quadprog Rcpp ExperimentHub dplyr impute PerformanceAnalytics Biobase ggpmisc tidyverse ggplot2 ggpubr minfi tibble RPMM stats graphics tidyr gridExtra preprocessCore dynamicTreeCut planet Ecume: caret dplyr e1071 kernlab magrittr methods pbapply spatstat.univar stats transport BSgenome.Hsapiens.UCSC.hg18: BSgenome BSgenome.Hsapiens.UCSC.hg19: BSgenome ROTS: Rcpp stats Biobase methods BiocParallel lme4 MouseThymusAgeing: SingleCellExperiment SummarizedExperiment ExperimentHub methods BiocGenerics S4Vectors IlluminaHumanMethylation450kmanifest: minfi ctsGE: ccaPP ggplot2 limma reshape2 shiny stats stringr utils traseR: GenomicRanges IRanges BSgenome.Hsapiens.UCSC.hg19 gamm4: methods Matrix lme4 mgcv h5mread: methods rhdf5 BiocGenerics SparseArray stats tools rhdf5filters S4Vectors IRanges S4Arrays Rhdf5lib HELP: stats graphics grDevices Biobase methods TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts: GenomicFeatures AnnotationDbi robustbase: stats graphics utils methods DEoptimR biocthis: BiocManager fs glue rlang styler usethis Guitar: GenomicFeatures rtracklayer AnnotationDbi GenomicRanges magrittr ggplot2 methods stats utils knitr dplyr TADCompare: dplyr PRIMME cluster Matrix magrittr HiCcompare ggplot2 tidyr ggpubr RColorBrewer reshape2 cowplot viridis: viridisLite ggplot2 gridExtra rsemmed: igraph methods magrittr stringr dplyr Delaporte: stats parallel hgu133a2.db: methods AnnotationDbi org.Hs.eg.db flowStats: BiocGenerics MASS flowCore flowWorkspace ncdfFlow flowViz fda Biobase methods grDevices graphics stats cluster utils KernSmooth lattice ks RColorBrewer rrcov corpcor mnormt clue 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 lifecycle simpleSeg rlang MSstatsLOBD: minpack.lm ggplot2 utils stats grDevices Rcpp RLassoCox: glmnet Matrix igraph survival stats HiCDCPlus: Rcpp InteractionSet GenomicInteractions bbmle pscl BSgenome data.table dplyr tidyr GenomeInfoDb rlang splines MASS GenomicRanges IRanges tibble R.utils Biostrings rtracklayer methods S4Vectors infinityFlow: flowCore stats grDevices utils graphics pbapply matlab png raster grid uwot gtools Biobase generics parallel methods xgboost spqn: ggplot2 ggridges SummarizedExperiment BiocGenerics graphics stats utils matrixStats BSgenome.Hsapiens.UCSC.hg38: GenomeInfoDb BSgenome alevinQC: rmarkdown tools methods ggplot2 GGally dplyr rjson shiny shinydashboard DT stats utils tximport cowplot rlang Rcpp LRcell: ExperimentHub AnnotationHub BiocParallel dplyr ggplot2 ggrepel magrittr stats utils RVenn: ggforce ggplot2 magrittr purrr methods rlang vegan pheatmap 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stats tidytree utils scQTLtools: ggplot2 Matrix stats progress stringr dplyr SeuratObject methods magrittr patchwork DESeq2 VGAM limma biomaRt gamlss SingleCellExperiment SummarizedExperiment GOSemSim BSgenome.Drerio.UCSC.danRer10: BSgenome digest: utils COSNet: NanoStringDiff: Biobase matrixStats methods Rcpp tidydr: ggfun ggplot2 grid rlang utils Rcollectl: utils ggplot2 lubridate processx KEGGlincs: KOdata hgu133a.db org.Hs.eg.db AnnotationDbi KEGGgraph igraph plyr gtools httr RJSONIO KEGGREST methods graphics stats utils XML grDevices flowMerge: graph feature flowClust Rgraphviz foreach snow rrcov flowCore graphics methods stats utils GenomicFiles: methods BiocGenerics MatrixGenerics GenomicRanges SummarizedExperiment BiocParallel Rsamtools rtracklayer GenomicAlignments IRanges S4Vectors VariantAnnotation GenomeInfoDb swamp: impute amap gplots MASS methods GWASExactHW: NMFN: planttfhunter: Biostrings SummarizedExperiment utils methods coMET: grid utils biomaRt Gviz psych hash 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BiocGenerics ComplexHeatmap consensusOV cowplot DGEobj.utils dplyr ensembldb ggplot2 ggridges GSVA IRanges magrittr matrixStats maxstat methods openair org.Hs.eg.db patchwork RColorBrewer TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene SpatialExperiment stats scales SummarizedExperiment survival survminer viridis AMARETTO: impute doParallel grDevices dplyr methods ComplexHeatmap callr Matrix Rcpp BiocFileCache DT MultiAssayExperiment circlize curatedTCGAData foreach glmnet httr limma matrixStats readr reshape2 tibble rmarkdown graphics grid parallel stats knitr ggplot2 gridExtra utils fansi: grDevices utils nucleoSim: stats IRanges S4Vectors graphics methods ridge: stats graphics grDevices utils m6Aboost: S4Vectors adabag GenomicRanges dplyr rtracklayer BSgenome Biostrings utils methods IRanges ExperimentHub RCircos: regioneReloaded: regioneR stats RColorBrewer Rtsne umap ggplot2 ggrepel reshape2 methods scales cluster grid grDevices safe: AnnotationDbi Biobase methods SparseM mgsub: logitnorm: rTensor: methods qqman: calibrate org.Pt.eg.db: methods AnnotationDbi sylly.en: sylly MGnifyR: MultiAssayExperiment TreeSummarizedExperiment SummarizedExperiment BiocGenerics mia ape dplyr httr methods plyr reshape2 S4Vectors urltools utils tidyjson antiProfilesData: Biobase alabaster.string: Biostrings alabaster.base utils methods S4Vectors HiCDataLymphoblast: TRONCO: bnlearn Rgraphviz gtools parallel foreach doParallel iterators RColorBrewer circlize igraph grid gridExtra xtable gtable scales R.matlab grDevices graphics stats utils methods pasillaBamSubset: geNetClassifier: Biobase EBarrays minet methods e1071 graphics grDevices interactiveDisplay: methods BiocGenerics grid interactiveDisplayBase shiny RColorBrewer ggplot2 reshape2 plyr gridSVG XML Category AnnotationDbi LRBaseDbi: methods stats utils AnnotationDbi RSQLite DBI Biobase gmoviz: circlize GenomicRanges graphics grid gridBase Rsamtools ComplexHeatmap BiocGenerics Biostrings GenomeInfoDb methods GenomicAlignments GenomicFeatures IRanges rtracklayer pracma colorspace S4Vectors skewr: methylumi wateRmelon mixsmsn IlluminaHumanMethylation450kmanifest minfi S4Vectors RColorBrewer MiRaGE: Biobase BiocGenerics S4Vectors AnnotationDbi BiocManager org.Ag.eg.db: methods AnnotationDbi waldo: cli diffobj glue methods rlang ggtreeSpace: interp ape dplyr GGally ggplot2 grid ggtree phytools rlang tibble tidyr tidyselect stats ITALICS: GLAD ITALICSData oligo affxparser pd.mapping50k.xba240 DBI oligoClasses stats TxDb.Rnorvegicus.UCSC.rn5.refGene: GenomicFeatures AnnotationDbi CSAR: S4Vectors IRanges GenomeInfoDb GenomicRanges stats utils CNVMetrics: GenomicRanges IRanges S4Vectors BiocParallel methods magrittr stats pheatmap gridExtra grDevices rBeta2009 pipeFrame: BSgenome digest visNetwork magrittr methods Biostrings GenomeInfoDb parallel stats utils rmarkdown fontquiver: fontBitstreamVera fontLiberation zeallot: consensus: RColorBrewer matrixStats gplots grDevices methods graphics stats utils alabama: numDeriv genomes: readr curl POMA: broom caret ComplexHeatmap dbscan dplyr DESeq2 fgsea FSA ggcorrplot ggplot2 ggrepel glmnet grid impute janitor limma lme4 magrittr MASS mixOmics multcomp msigdbr purrr randomForest RankProd rlang SummarizedExperiment sva tibble tidyr utils uwot vegan randPack: methods Biobase bnlearn: methods OncoScore: biomaRt grDevices graphics utils methods EnrichmentBrowser: SummarizedExperiment graph AnnotationDbi BiocFileCache BiocManager GSEABase GO.db KEGGREST KEGGgraph Rgraphviz S4Vectors SPIA edgeR graphite hwriter limma methods pathview safe HD2013SGI: RColorBrewer gplots geneplotter splots limma vcd LSD EBImage CCPROMISE: stats methods CCP PROMISE Biobase GSEABase utils rgenoud: utils snowfall: snow beanplot: chromPlot: stats utils graphics grDevices datasets base biomaRt GenomicRanges akima: sp phantasusLite: data.table rhdf5client httr stringr stats utils Biobase methods bestNormalize: LambertW nortest dplyr doParallel foreach doRNG recipes tibble methods butcher purrr generics BulkSignalR: BiocFileCache httr DBI RSQLite cli curl dplyr rlang jsonlite matrixStats methods doParallel glmnet ggalluvial ggplot2 gridExtra grid Rtsne ggrepel foreach multtest igraph orthogene stabledist circlize ComplexHeatmap stats scales RANN SpatialExperiment SummarizedExperiment tools 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 BioGA: ggplot2 graphics Rcpp SummarizedExperiment animation rlang biocViews sessioninfo BiocStyle CTexploreR: CTdata BiocGenerics ComplexHeatmap grid SummarizedExperiment GenomicRanges IRanges dplyr tidyr tibble ggplot2 rlang grDevices stats circlize ggrepel SingleCellExperiment MatrixGenerics calm: mgcv stats graphics TENxVisiumData: ExperimentHub SpatialExperiment utils crmn: pcaMethods Biobase methods PepsNMR: Matrix ptw ggplot2 gridExtra matrixStats reshape2 methods graphics stats proteinProfiles: graphics stats MSPrep: SummarizedExperiment S4Vectors pcaMethods crmn preprocessCore dplyr tidyr tibble magrittr rlang stats stringr methods missForest sva VIM PMA: utils CluMSIDdata: modeltools: stats stats4 methods TxDb.Hsapiens.UCSC.hg19.knownGene: GenomicFeatures AnnotationDbi pls: grDevices graphics methods stats ggpattern: cli ggplot2 glue grid gridpattern lifecycle rlang scales vctrs healthyFlowData: flowCore methods reldist: mgcv densEstBayes hgu133afrmavecs: storr: R6 digest ChemmineDrugs: ChemmineR BiocGenerics RSQLite 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 netDx: ROCR pracma ggplot2 glmnet igraph reshape2 parallel stats utils MultiAssayExperiment graphics grDevices methods BiocFileCache GenomicRanges bigmemory doParallel foreach combinat rappdirs GenomeInfoDb S4Vectors IRanges RColorBrewer Rtsne httr plotrix pmm: lme4 splines ClustAll: FactoMineR bigstatsr clValid doSNOW parallel foreach dplyr fpc mice modeest flock networkD3 methods ComplexHeatmap cluster RColorBrewer circlize grDevices ggplot2 grid stats utils pbapply tensor: pmp: stats impute pcaMethods missForest ggplot2 methods SummarizedExperiment S4Vectors matrixStats grDevices reshape2 utils downloader: utils digest EventPointer: SGSeq Matrix SummarizedExperiment GenomicFeatures stringr GenomeInfoDb igraph MASS nnls limma matrixStats RBGL prodlim graph methods utils stats doParallel foreach affxparser GenomicRanges S4Vectors IRanges qvalue cobs rhdf5 BSgenome Biostrings glmnet abind iterators lpSolve poibin speedglm tximport fgsea SpatialDecon: grDevices stats utils graphics SeuratObject Biobase GeomxTools repmis methods Matrix logNormReg maftools: data.table grDevices methods RColorBrewer Rhtslib survival DNAcopy pheatmap zlibbioc scReClassify: randomForest e1071 stats SummarizedExperiment SingleCellExperiment methods stringfish: Rcpp RcppParallel png: AnVILWorkflow: AnVILGCP AnVILBase httr AnVIL dplyr jsonlite rlang tibble tidyr utils methods plyr stringr SARC: RaggedExperiment GenomicRanges tidyverse utils reshape2 DescTools metap multtest plyranges data.table scales RColorBrewer grid gtable gridExtra GenomicFeatures stats ggplot2 plotly IRanges CBEA: BiocParallel BiocSet dplyr lmom fitdistrplus magrittr methods mixtools Rcpp stats SummarizedExperiment tibble TreeSummarizedExperiment tidyr glue generics rlang goftest dagitty: V8 jsonlite boot MASS methods grDevices stats utils graphics ParallelLogger: snow xml2 jsonlite methods utils CATT: stats RcppHungarian: Rcpp QDNAseq.mm10: QDNAseq tsne: preprocessCore: stats infotheo: cypress: stats abind sirt MASS TOAST tibble parallel preprocessCore SummarizedExperiment TCA PROPER methods dplyr utils RColorBrewer graphics edgeR BiocParallel checkmate mvtnorm DESeq2 rlang e1071 gert: askpass credentials openssl rstudioapi sys zip CleanUpRNAseq: AnnotationFilter BiocGenerics Biostrings BSgenome DESeq2 edgeR ensembldb GenomeInfoDb GenomicRanges ggplot2 ggrepel graphics grDevices KernSmooth limma methods pheatmap qsmooth R6 RColorBrewer Rsamtools Rsubread reshape2 SummarizedExperiment stats tximport utils zlibbioc: igvR: GenomicRanges GenomicAlignments BrowserViz methods BiocGenerics httpuv utils rtracklayer VariantAnnotation RColorBrewer httr AMOUNTAIN: stats spatialDE: reticulate basilisk checkmate stats SpatialExperiment methods SummarizedExperiment Matrix ggplot2 ggrepel scales gridExtra BiocGenerics: methods utils graphics stats generics Icens: survival graphics lavaan: methods stats4 stats utils graphics MASS mnormt pbivnorm numDeriv quadprog MetaCycle: gnm TxDb.Hsapiens.UCSC.hg18.knownGene: GenomicFeatures AnnotationDbi rTRMui: shiny rTRM MotifDb org.Hs.eg.db org.Mm.eg.db biglm: DBI methods ChIPXpress: ChIPXpressData Biobase GEOquery frma affy bigmemory biganalytics