MatrixGenerics: matrixStats methods SomaDataIO: cli dplyr ggplot2 lifecycle magrittr methods readxl tibble tidyr httr: curl jsonlite mime openssl R6 EPICv2manifest: AnnotationHub tidyr: cli dplyr glue lifecycle magrittr purrr rlang stringr tibble tidyselect utils vctrs cpp11 jsonlite: methods AnnotationHub: BiocGenerics BiocFileCache utils methods grDevices RSQLite BiocManager BiocVersion curl rappdirs AnnotationDbi S4Vectors httr2 yaml dplyr BiocBaseUtils org.Mxanthus.db: methods AnnotationHub AnnotationDbi BiocStyle BiocFileCache gtools: methods stats utils Formula: stats blob: methods rlang vctrs RBGL: graph methods BH derfinder: BiocGenerics AnnotationDbi BiocParallel bumphunter derfinderHelper Seqinfo GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges methods qvalue Rsamtools rtracklayer S4Vectors stats utils sparsevctrs: cli rlang vctrs RSQLite: bit64 blob DBI memoise methods pkgconfig rlang plogr cpp11 pillar: cli glue lifecycle rlang utf8 utils vctrs quantreg: stats SparseM methods graphics Matrix MatrixModels survival MASS ggsignif: ggplot2 XVector: methods BiocGenerics S4Vectors IRanges utils stats tools promises: fastmap later lifecycle magrittr otel R6 rlang polyclip: gson: jsonlite methods rlang stats tidyr utils recipes: dplyr cli clock generics glue gower hardhat ipred lifecycle lubridate magrittr Matrix purrr rlang sparsevctrs stats tibble tidyr tidyselect timeDate utils vctrs withr plyr: Rcpp R.oo: R.methodsS3 methods utils OrganismDbi: BiocGenerics AnnotationDbi Seqinfo GenomicFeatures methods utils stats DBI BiocManager Biobase graph RBGL S4Vectors IRanges GenomicRanges ggnewscale: ggplot2 cadd.v1.6.hg19: GenomicScores AnnotationHub bibtex: backports utils affxparser: UCSCRepeatMasker: GenomicRanges AnnotationHub GenomeInfoDb XML RCurl bookdown: htmltools knitr rmarkdown jquerylib xfun tinytex yaml TENET.AnnotationHub: AnnotationHub GenomicRanges tidytree: ape dplyr lazyeval magrittr methods rlang tibble tidyr tidyselect yulab.utils pillar cli tweenr: farver magrittr rlang vctrs cpp11 km.ci: stats survival jpeg: SomaScan.db: AnnotationDbi methods DBI org.Hs.eg.db MatrixModels: stats methods Matrix downlit: brio desc digest evaluate fansi memoise rlang vctrs withr yaml BiocParallel: methods stats utils futile.logger parallel snow codetools BH cpp11 openssl: askpass timechange: cpp11 usethis: cli clipr crayon curl desc fs gert gh glue jsonlite lifecycle purrr rappdirs rlang rprojroot rstudioapi stats tools utils whisker withr yaml ggtangle: ggfun ggplot2 ggrepel igraph rlang yulab.utils cachem: rlang fastmap JASPAR2020: methods ROCR: methods graphics grDevices gplots stats TFMPvalue: Rcpp quantmod: xts zoo TTR methods curl jsonlite pbkrtest: lme4 broom dplyr MASS methods numDeriv Matrix doBy JASPAR2022: methods BiocFileCache utils cli: utils deldir: graphics grDevices forecast: colorspace fracdiff generics ggplot2 graphics lmtest magrittr nnet parallel Rcpp stats timeDate tseries urca withr zoo RcppArmadillo JASPAR2024: methods BiocFileCache utils DOSE: AnnotationDbi BiocParallel fgsea ggplot2 GOSemSim methods qvalue reshape2 stats utils yulab.utils ggtext: ggplot2 grid gridtext rlang scales memoise: rlang cachem evaluate: methods: utils stats R.methodsS3: utils parallelly: parallel tools utils rstatix: stats utils tidyr purrr broom rlang tibble dplyr magrittr corrplot tidyselect car generics foreign: methods utils stats httr2: cli curl glue lifecycle magrittr openssl R6 rappdirs rlang vctrs withr graph: methods BiocGenerics stats stats4 utils tools: TCGAbiolinks: downloader grDevices biomaRt dplyr graphics tibble GenomicRanges XML data.table jsonlite plyr knitr methods ggplot2 stringr IRanges rvest stats utils S4Vectors R.utils SummarizedExperiment TCGAbiolinksGUI.data readr tools tidyr purrr xml2 httr BiocStyle: bookdown knitr rmarkdown stats utils yaml BiocManager GlobalOptions: methods utils BiocIO: BiocGenerics S4Vectors methods tools matlab: methods HPO.db: AnnotationDbi AnnotationHub BiocFileCache DBI methods utils plyranges: BiocGenerics IRanges GenomicRanges dplyr methods rlang magrittr tidyselect rtracklayer GenomicAlignments Seqinfo Rsamtools S4Vectors utils AHWikipathwaysDbs: AnnotationHub locfit: lattice cluster: graphics grDevices stats utils irlba: Matrix stats methods lambda.r: formatR compiler: scAnnotatR.models: tinytex: xfun caTools: bitops grid: grDevices utils MotifDb: methods BiocGenerics S4Vectors IRanges GenomicRanges Biostrings rtracklayer splitstackshape ggridges: ggplot2 grid scales withr GeneSummary: igraph: methods cli graphics grDevices lifecycle magrittr Matrix pkgconfig rlang stats utils vctrs cpp11 labeling: stats graphics gtable: cli glue grid lifecycle rlang stats knitr: evaluate highr methods tools xfun yaml fastmap: future.apply: future globals parallel utils uwot: Matrix FNN irlba methods Rcpp RcppAnnoy RSpectra dqrng RcppProgress commonmark: KernSmooth: stats readr: cli clipr crayon hms lifecycle methods R6 rlang tibble utils vroom cpp11 tzdb otel: frma: Biobase MASS DBI affy methods oligo oligoClasses preprocessCore utils BiocGenerics scAnnotatR: Seurat SingleCellExperiment SummarizedExperiment dplyr ggplot2 caret ROCR pROC data.tree methods stats e1071 ape kernlab AnnotationHub utils fastDummies: data.table tibble stringr lmtest: stats zoo graphics urlchecker: cli curl tools xml2 BSgenome.Hsapiens.UCSC.hg38: GenomeInfoDb BSgenome sass: fs rlang htmltools R6 rappdirs vroom: bit64 cli crayon glue hms lifecycle methods rlang stats tibble tidyselect tzdb vctrs withr cpp11 progress foreach: codetools utils iterators splines: graphics stats carData: prodlim: Rcpp stats rlang data.table grDevices ggplot2 graphics diagram survival KernSmooth lava TENET.ExperimentHub: ggplot2 ExperimentHub SummarizedExperiment MultiAssayExperiment GenomicRanges methods Rdpack: methods tools utils rbibutils BiocFileCache: dbplyr methods stats utils dplyr RSQLite DBI filelock curl httr2 dqrng: Rcpp BH sitmo litedown: utils commonmark xfun DirichletMultinomial: S4Vectors IRanges stats4 methods BiocGenerics progress: crayon hms prettyunits R6 ggrepel: ggplot2 grid Rcpp rlang scales withr backports: lattice: grid grDevices graphics stats utils biovizBase: methods grDevices stats scales Hmisc RColorBrewer dichromat BiocGenerics S4Vectors IRanges Seqinfo GenomeInfoDb GenomicRanges SummarizedExperiment Biostrings Rsamtools GenomicAlignments GenomicFeatures AnnotationDbi VariantAnnotation ensembldb AnnotationFilter rlang RcppEigen: Rcpp stats utils checkmate: backports utils Structstrings: S4Vectors IRanges Biostrings methods BiocGenerics XVector stringr stringi crayon grDevices GenomicRanges: methods stats4 BiocGenerics S4Vectors IRanges Seqinfo utils stats minqa: Rcpp qvalue: splines ggplot2 grid reshape2 rat2302frmavecs: affy frma pwalign: BiocGenerics S4Vectors IRanges Biostrings methods utils XVector rvest: cli glue httr lifecycle magrittr rlang selectr tibble xml2 colorspace: methods graphics grDevices stats ggbio: methods BiocGenerics ggplot2 grid grDevices graphics stats utils gridExtra scales reshape2 gtable Hmisc biovizBase Biobase S4Vectors IRanges Seqinfo GenomeInfoDb GenomicRanges SummarizedExperiment Biostrings Rsamtools GenomicAlignments BSgenome VariantAnnotation rtracklayer GenomicFeatures OrganismDbi ensembldb AnnotationDbi AnnotationFilter rlang ggfun: cli dplyr ggplot2 grid rlang scales utils yulab.utils EpiTxDb.Sc.sacCer3: AnnotationHub EpiTxDb tRNA: GenomicRanges Structstrings stringr S4Vectors methods BiocGenerics IRanges XVector Biostrings Modstrings ggplot2 scales preprocessCore: stats timeDate: methods graphics utils stats clipr: utils devtools: usethis cli desc ellipsis fs lifecycle memoise miniUI pkgbuild pkgdown pkgload profvis rcmdcheck remotes rlang roxygen2 rversions sessioninfo stats testthat tools urlchecker utils withr BiocBaseUtils: methods utils GetoptLong: rjson GlobalOptions methods crayon synaptome.data: AnnotationHub dir.expiry: utils filelock caret: ggplot2 lattice e1071 foreach grDevices methods ModelMetrics nlme plyr pROC recipes reshape2 stats stats4 utils withr gitcreds: GO.db: methods AnnotationDbi snow: utils scales: cli farver glue labeling lifecycle R6 RColorBrewer rlang viridisLite fontawesome: rlang htmltools tensor: whisker: HDF5Array: methods SparseArray DelayedArray h5mread utils stats tools Matrix BiocGenerics S4Vectors IRanges S4Arrays rhdf5 RSpectra: Matrix Rcpp RcppEigen gower: sesame: sesameData graphics BiocParallel utils methods stringr readr tibble MASS wheatmap GenomicRanges IRanges grid preprocessCore S4Vectors ggplot2 BiocFileCache Seqinfo stats SummarizedExperiment dplyr reshape2 affyio: methods ff: bit utils lme4: Matrix methods stats graphics grid splines utils parallel MASS lattice boot nlme minqa nloptr reformulas rlang Rdpack Rcpp RcppEigen enrichplot: aplot DOSE ggfun ggnewscale ggplot2 ggrepel ggtangle graphics grid igraph methods plyr purrr RColorBrewer reshape2 rlang stats tidydr utils scatterpie GOSemSim ggtree yulab.utils biocViews: Biobase graph methods RBGL tools utils XML RCurl RUnit BiocManager tibble: cli lifecycle magrittr methods pillar pkgconfig rlang utils vctrs AnnotationHubData: methods utils S4Vectors IRanges GenomicRanges AnnotationHub GenomicFeatures Rsamtools rtracklayer BiocGenerics jsonlite BiocManager biocViews BiocCheck graph AnnotationDbi Biobase Biostrings DBI Seqinfo GenomeInfoDb OrganismDbi RSQLite AnnotationForge futile.logger XML RCurl IRanges: methods utils stats BiocGenerics S4Vectors stats4 ellipsis: rlang GenomicFeatures: BiocGenerics S4Vectors IRanges Seqinfo GenomicRanges AnnotationDbi methods utils stats DBI XVector Biostrings rtracklayer credentials: openssl sys curl jsonlite askpass nnet: stats utils synaptome.db: synaptome.data DBI RSQLite dplyr dbplyr igraph Rdpack AnnotationHub utils BioMartGOGeneSets: utils S4Vectors GenomicRanges mime: tools future: digest globals listenv parallel parallelly utils fs: methods plogr: nlme: graphics stats utils lattice MASS: grDevices graphics stats utils methods metaboliteIDmapping: AnnotationHub AHPathbankDbs: AnnotationHub alternativeSplicingEvents.hg19: AnnotationHub class: stats utils MASS progressr: digest utils RcppProgress: profvis: htmlwidgets rlang vctrs gh: cli gitcreds glue httr2 ini jsonlite lifecycle rlang hms: cli lifecycle methods pkgconfig rlang vctrs matrixStats: gert: askpass credentials openssl rstudioapi sys zip stringr: cli glue lifecycle magrittr rlang stringi vctrs Rhdf5lib: kernlab: methods stats grDevices graphics plotly: ggplot2 tools scales httr jsonlite magrittr digest viridisLite base64enc htmltools htmlwidgets tidyr RColorBrewer dplyr vctrs tibble lazyeval rlang crosstalk purrr data.table promises RcppHNSW: methods Rcpp SparseArray: methods Matrix BiocGenerics MatrixGenerics S4Vectors S4Arrays utils stats matrixStats IRanges XVector DelayedArray: methods stats4 Matrix BiocGenerics MatrixGenerics S4Vectors IRanges S4Arrays SparseArray stats rversions: curl cigarillo: methods BiocGenerics S4Vectors IRanges Biostrings stats stats: utils grDevices graphics rex: lazyeval GenomeInfoDb: methods BiocGenerics S4Vectors IRanges Seqinfo stats utils UCSC.utils survminer: ggplot2 ggpubr grid gridExtra magrittr maxstat methods scales survival stats broom dplyr tidyr survMisc purrr tibble rlang ggtext AlphaMissense.v2023.hg19: GenomicScores AnnotationHub covr: methods digest stats utils jsonlite rex httr cli withr yaml rlang: utils rhdf5: methods Rhdf5lib rhdf5filters futile.logger: utils lambda.r futile.options RCurl: methods bitops iterators: utils goftest: stats RcppAnnoy: methods Rcpp base64enc: bitops: testthat: brio callr cli desc evaluate jsonlite lifecycle magrittr methods pkgload praise processx ps R6 rlang utils waldo withr 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 ExperimentHub: methods BiocGenerics AnnotationHub BiocFileCache utils S4Vectors BiocManager rappdirs GenomicScores: S4Vectors GenomicRanges methods BiocGenerics stats utils XML httr Biobase BiocManager BiocFileCache IRanges Biostrings Seqinfo GenomeInfoDb AnnotationHub rhdf5 DelayedArray HDF5Array abind: methods utils reshape2: plyr Rcpp stringr R6: lubridate: methods generics timechange bit: survMisc: survival graphics grDevices stats utils knitr KMsurv ggplot2 data.table zoo grid gridExtra km.ci xtable filelock: rprojroot: Hmisc: methods ggplot2 cluster rpart nnet foreign gtable grid gridExtra data.table htmlTable viridisLite htmltools base64enc colorspace rmarkdown knitr Formula exactRankTests: stats utils stringi: tools utils stats alternativeSplicingEvents.hg38: AnnotationHub png: Seqinfo: methods BiocGenerics stats S4Vectors IRanges geneplast: methods igraph snow ape grDevices graphics stats utils data.table here: rprojroot microbenchmark: graphics stats S7: utils bumphunter: S4Vectors IRanges Seqinfo GenomicRanges foreach iterators methods parallel locfit matrixStats limma doRNG BiocGenerics utils GenomicFeatures AnnotationDbi stats diffobj: crayon tools methods utils stats statmod: stats graphics askpass: sys highr: xfun AHPubMedDbs: AnnotationHub AlphaMissense.v2023.hg38: GenomicScores AnnotationHub doRNG: foreach rngtools stats utils iterators fontLiberation: doBy: methods boot broom cowplot Deriv dplyr forecast ggplot2 MASS Matrix modelr microbenchmark rlang purrr tibble tidyr remotes: methods stats tools utils gdtools: fontquiver htmltools Rcpp systemfonts tools sessioninfo: cli tools utils quadprog: reticulate: Matrix Rcpp RcppTOML graphics here jsonlite methods png rappdirs utils rlang withr CENTREannotation: AnnotationHub RSQLite DBI BiocGenerics methods gridtext: curl grid grDevices markdown rlang Rcpp png jpeg stringr xml2 oligoClasses: BiocGenerics Biobase methods graphics IRanges GenomicRanges SummarizedExperiment Biostrings affyio foreach BiocManager utils S4Vectors RSQLite DBI ff fontBitstreamVera: pkgconfig: utils sesameData: ExperimentHub AnnotationHub utils readr stringr GenomicRanges S4Vectors IRanges Seqinfo SparseM: methods graphics stats utils xtable: stats utils RCircos: spatstat.explore: spatstat.data spatstat.univar spatstat.geom spatstat.random stats graphics grDevices utils methods nlme spatstat.utils spatstat.sparse goftest Matrix abind patchwork: ggplot2 gtable grid stats grDevices utils graphics rlang cli farver ggplotify: ggplot2 graphics grDevices grid gridGraphics rlang yulab.utils brew: Rtsne: Rcpp stats lava: cli future.apply graphics grDevices methods numDeriv progressr stats survival SQUAREM utils tzdb: cpp11 cpp11: KMsurv: annotate: AnnotationDbi XML Biobase DBI xtable graphics utils stats methods BiocGenerics httr KEGGREST: methods httr png Biostrings spatstat.random: spatstat.data spatstat.univar spatstat.geom stats utils methods grDevices spatstat.utils excluderanges: GenomicRanges urca: methods nlme graphics stats SeuratObject: sp future future.apply generics grDevices grid lifecycle Matrix methods progressr Rcpp rlang spam stats tools utils RcppEigen wheatmap: grid stats colorspace RColorBrewer TFBSTools: Biobase Biostrings pwalign BiocGenerics BiocParallel BSgenome caTools DirichletMultinomial Seqinfo GenomicRanges gtools grid IRanges methods DBI RSQLite rtracklayer seqLogo S4Vectors TFMPvalue XML XVector parallel BiocGenerics: methods utils graphics stats generics survival: graphics Matrix methods splines stats utils readxl: cellranger tibble utils cpp11 progress data.tree: R6 stringi methods clock: cli lifecycle rlang tzdb vctrs cpp11 MPO.db: AnnotationDbi AnnotationHub BiocFileCache DBI methods utils ica: FNN: CTCF: data.table: methods fitdistrplus: MASS grDevices survival methods stats rlang AHLRBaseDbs: AnnotationHub S4Vectors: methods utils stats stats4 BiocGenerics ggtree: ape aplot dplyr ggplot2 grid magrittr methods purrr rlang ggfun yulab.utils tidyr tidytree treeio utils scales stats cli ggiraph zip: tRNAdbImport: GenomicRanges Modstrings Structstrings tRNA Biostrings stringr httr2 xml2 S4Vectors methods IRanges utils Biostrings: BiocGenerics S4Vectors IRanges XVector Seqinfo methods utils grDevices stats crayon ensembldb: BiocGenerics GenomicRanges GenomicFeatures AnnotationFilter methods RSQLite DBI Biobase Seqinfo GenomeInfoDb AnnotationDbi rtracklayer S4Vectors Rsamtools IRanges ProtGenerics Biostrings curl Deriv: methods rjson: miniUI: shiny htmltools utils fracdiff: stats derfinderHelper: IRanges Matrix methods S4Vectors h5mread: methods rhdf5 BiocGenerics SparseArray stats tools rhdf5filters S4Vectors IRanges S4Arrays Rhdf5lib polynom: stats graphics GenomicAlignments: methods BiocGenerics S4Vectors IRanges Seqinfo GenomicRanges SummarizedExperiment Biostrings Rsamtools utils stats BiocParallel cigarillo futile.options: ragg: systemfonts textshaping SQUAREM: Rcpp: methods utils EuPathDB: Biobase GenomicRanges GenomeInfoDbData AnnotationHub AnnotationHubData Biostrings BiocManager utils Biobase: BiocGenerics utils methods pkgload: cli desc fs glue lifecycle methods pkgbuild processx rlang rprojroot utils bit64: bit graphics methods stats utils maxstat: exactRankTests mvtnorm stats graphics viridisLite: dotCall64: brio: GenomicFiles: BiocGenerics BiocParallel GenomicRanges MatrixGenerics methods Rsamtools rtracklayer SummarizedExperiment BiocBaseUtils GenomeInfoDb GenomicAlignments IRanges S4Vectors Seqinfo VariantAnnotation TTR: xts zoo curl conflicted: cli memoise rlang stats4: graphics methods stats BiocManager: utils yulab.utils: cli digest fs rappdirs rlang tools utils selectr: methods stringr R6 cellranger: rematch tibble spatstat.geom: spatstat.data spatstat.univar stats graphics grDevices utils methods spatstat.utils deldir polyclip yaml: globals: codetools numDeriv: RUnit: utils methods graphics limma: grDevices graphics stats utils methods statmod UniProtKeywords: utils ontoProcData: RefManageR: xml2 jsonlite utils plyr tools httr lubridate stringr methods bibtex httpuv: later promises R6 Rcpp utils UCSC.utils: methods stats httr jsonlite S4Vectors spatstat.sparse: stats utils methods Matrix abind tensor spatstat.utils clusterProfiler: AnnotationDbi DOSE dplyr enrichplot GO.db GOSemSim gson httr igraph magrittr methods plyr qvalue rlang stats tidyr utils yulab.utils listenv: biomaRt: methods AnnotationDbi BiocFileCache curl httr2 progress stringr utils xml2 purrr: cli lifecycle magrittr rlang vctrs RANN: stringdist: parallel GenomicState: AnnotationHub Seqinfo GenomicFeatures rtracklayer bumphunter derfinder AnnotationDbi IRanges org.Hs.eg.db utils methods txdbmaker MultiAssayExperiment: SummarizedExperiment Biobase BiocBaseUtils BiocGenerics DelayedArray GenomicRanges IRanges MatrixGenerics methods S4Vectors tidyr utils fontquiver: fontBitstreamVera fontLiberation htmlTable: stringr knitr magrittr methods checkmate htmlwidgets htmltools rstudioapi proxy: stats utils derfinderPlot: derfinder Seqinfo GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 graphics grDevices IRanges limma methods plyr RColorBrewer reshape2 S4Vectors scales utils mgcv: nlme methods stats graphics Matrix splines utils car: carData abind Formula MASS mgcv nnet pbkrtest quantreg grDevices utils stats graphics lme4 nlme scales generics: methods TCGAbiolinksGUI.data: SummarizedExperiment: methods MatrixGenerics GenomicRanges Biobase utils stats tools Matrix BiocGenerics S4Vectors IRanges Seqinfo S4Arrays DelayedArray oligo: BiocGenerics oligoClasses Biobase Biostrings affyio affxparser DBI ff graphics methods preprocessCore RSQLite splines stats stats4 utils bit RcppTOML: Rcpp BAMMtools: ape Rcpp gplots methods org.Hbacteriophora.eg.db: methods AnnotationDbi DBI ps: utils fansi: grDevices utils PANTHER.db: AnnotationDbi AnnotationHub utils methods RSQLite BiocFileCache gplots: gtools stats caTools KernSmooth methods AHMeSHDbs: AnnotationHub xts: zoo methods utils: pkgbuild: callr cli desc processx R6 textshaping: lifecycle stats stringi systemfonts utils cpp11 TENET: graphics grDevices stats utils tools S4Vectors GenomicRanges IRanges parallel pastecs ggplot2 RCircos survival BSgenome.Hsapiens.UCSC.hg38 seqLogo Biostrings matlab TCGAbiolinks methods R.utils MultiAssayExperiment SummarizedExperiment sesame sesameData AnnotationHub ExperimentHub TENET.ExperimentHub rtracklayer MotifDb BAMMtools survminer org.Hs.eg.db: methods AnnotationDbi formatR: lifecycle: cli glue rlang Rhtslib: tools xopen: processx ggsci: ggplot2 grDevices rlang scales callr: processx R6 utils AnnotationDbi: methods stats4 BiocGenerics Biobase IRanges DBI RSQLite S4Vectors stats KEGGREST pastecs: boot stats graphics utils grDevices pkgdown: bslib callr cli desc downlit fontawesome fs httr2 jsonlite lifecycle openssl purrr ragg rlang rmarkdown tibble whisker withr xml2 yaml e1071: graphics grDevices class stats methods utils proxy gridGraphics: grid graphics grDevices systemfonts: base64enc grid jsonlite lifecycle tools utils cpp11 sys: rGenomeTracksData: AnnotationHub rstudioapi: htmlwidgets: grDevices htmltools jsonlite knitr rmarkdown yaml graphics: grDevices waldo: cli diffobj glue methods rlang tidydr: cluster ggfun ggplot2 grid rlang stats utils S4Arrays: methods Matrix abind BiocGenerics S4Vectors IRanges stats restfulr: methods XML RCurl rjson S4Vectors yaml roxygen2: brew cli commonmark desc knitr methods pkgload purrr R6 rlang stringi stringr utils withr xml2 cpp11 sets: graphics grDevices stats utils DBI: methods markdown: utils xfun litedown geneplast.data: ape treeio tibble tidyr dplyr readr purrr igraph geneplast BiocFileCache zoo: stats utils graphics grDevices lattice seqLogo: methods grid stats4 grDevices dplyr: cli generics glue lifecycle magrittr methods pillar R6 rlang tibble tidyselect utils vctrs utf8: BH: treeio: ape dplyr jsonlite magrittr methods rlang stats tibble tidytree utils yulab.utils shape: stats graphics grDevices vctrs: cli glue lifecycle rlang dbplyr: blob cli DBI dplyr glue lifecycle magrittr methods pillar purrr R6 rlang tibble tidyr tidyselect utils vctrs withr BiocCheck: BiocBaseUtils BiocFileCache BiocManager biocViews callr cli codetools graph httr2 knitr methods rvest stringdist tools utils tseries: graphics stats utils quadprog zoo quantmod jsonlite R.utils: R.oo methods utils tools R.methodsS3 modelr: broom magrittr purrr rlang tibble tidyr tidyselect vctrs bslib: base64enc cachem fastmap grDevices htmltools jquerylib jsonlite lifecycle memoise mime rlang sass shiny: methods bslib cachem cli commonmark fastmap fontawesome glue grDevices htmltools httpuv jsonlite later lifecycle mime otel promises R6 rlang sourcetools tools utils withr xtable sitmo: Rcpp sp: methods utils stats graphics grDevices lattice grid affy: BiocGenerics Biobase affyio BiocManager graphics grDevices methods preprocessCore stats utils grDevices: pander: grDevices graphics methods utils stats digest tools Rcpp AHEnsDbs: methods ensembldb AnnotationHubData Rsamtools: methods Seqinfo GenomicRanges Biostrings utils BiocGenerics S4Vectors IRanges XVector bitops BiocParallel stats Rhtslib BSgenome: methods BiocGenerics S4Vectors IRanges Seqinfo GenomicRanges Biostrings BiocIO rtracklayer utils stats matrixStats XVector Rsamtools GenomeInfoDbData: corrplot: ipred: rpart MASS survival nnet class prodlim BiocVersion: diagram: shape stats graphics reformulas: stats methods Matrix Rdpack glue: methods downloader: utils digest digest: utils pROC: methods Rcpp RColorBrewer: rbibutils: utils tools hardhat: cli glue rlang sparsevctrs tibble vctrs Matrix: methods grDevices graphics grid lattice stats utils 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cowplot ggsignif scales gridExtra glue polynom rlang rstatix tibble magrittr withr: graphics grDevices sourcetools: leidenbase: igraph pbapply: parallel lazyeval: magrittr: EpiTxDb.Hs.hg38: AnnotationHub EpiTxDb crayon: grDevices methods utils splitstackshape: data.table txdbmaker: BiocGenerics S4Vectors Seqinfo GenomicRanges GenomicFeatures methods utils stats tools httr rjson DBI RSQLite IRanges UCSC.utils GenomeInfoDb AnnotationDbi Biobase BiocIO rtracklayer biomaRt Modstrings: Biostrings methods BiocGenerics GenomicRanges S4Vectors IRanges XVector stringi stringr crayon grDevices gwascatData: data.table RcppArmadillo: Rcpp stats utils methods AHCytoBands: methods xml2: cli methods rlang praise: prettyunits: aplot: ggfun ggplot2 ggplotify patchwork magrittr methods utils yulab.utils pillar rngtools: methods digest utils stats parallel spatstat.univar: stats spatstat.utils graphics isoband: cli grid rlang utils cpp11 jquerylib: htmltools nloptr: ENCODExplorerData: tools jsonlite RCurl data.table methods hpAnnot: AnnotationHub scattermore: ggplot2 scales grid grDevices graphics rhdf5filters: Rhdf5lib dichromat: stats spam: dotCall64 grid methods Rcpp AnnotationForge: methods utils BiocGenerics Biobase AnnotationDbi DBI RSQLite XML S4Vectors RCurl VariantAnnotation: methods BiocGenerics MatrixGenerics Seqinfo GenomicRanges SummarizedExperiment Rsamtools utils DBI Biobase S4Vectors IRanges XVector Biostrings AnnotationDbi rtracklayer BSgenome GenomicFeatures curl Rhtslib rappdirs: SingleCellExperiment: SummarizedExperiment methods utils stats S4Vectors BiocGenerics GenomicRanges DelayedArray crosstalk: htmltools jsonlite lazyeval R6 rmarkdown: bslib evaluate fontawesome htmltools jquerylib jsonlite knitr methods tinytex tools utils xfun yaml boot: graphics stats ModelMetrics: Rcpp data.table codetools: curl: rematch: cadd.v1.6.hg38: GenomicScores AnnotationHub ini: gridExtra: gtable grid grDevices graphics utils ggiraph: cli dplyr gdtools ggplot2 grid htmltools htmlwidgets purrr Rcpp rlang S7 stats systemfonts vctrs rtracklayer: methods GenomicRanges XML BiocGenerics S4Vectors IRanges XVector Seqinfo Biostrings curl httr Rsamtools GenomicAlignments BiocIO tools restfulr EpiTxDb.Mm.mm10: AnnotationHub EpiTxDb graphite: methods AnnotationDbi graph httr rappdirs stats utils graphics rlang lifecycle purrr dir.expiry fastmatch: fgsea: Rcpp data.table BiocParallel stats ggplot2 cowplot grid fastmatch Matrix scales utils BH ProtGenerics: methods desc: cli R6 utils ape: nlme lattice graphics methods stats utils parallel Rcpp digest GOSemSim: AnnotationDbi DBI digest GO.db methods rlang R.utils stats utils yulab.utils Rcpp EpiTxDb: AnnotationDbi Modstrings methods utils httr xml2 curl rex GenomicFeatures txdbmaker GenomicRanges Seqinfo BiocGenerics BiocFileCache S4Vectors IRanges RSQLite DBI Biostrings tRNAdbImport spatstat.data: spatstat.utils Matrix parallel: tools compiler sctransform: dplyr magrittr MASS Matrix methods future.apply future ggplot2 reshape2 rlang gridExtra matrixStats RcppArmadillo Rcpp rpart: graphics stats grDevices xfun: grDevices stats tools tidyselect: cli glue lifecycle rlang vctrs withr scatterpie: ggplot2 ggforce rlang ggfun stats tidyr dplyr utils yulab.utils