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vctrs withr TxDb.Hsapiens.UCSC.hg18.knownGene: GenomicFeatures AnnotationDbi timechange: cpp11 igraph: methods cli graphics grDevices lifecycle magrittr Matrix pkgconfig rlang stats utils vctrs cpp11 ObMiTi: SummarizedExperiment ExperimentHub Rlab: utils stats PasillaTranscriptExpr: rtracklayer: methods GenomicRanges XML BiocGenerics S4Vectors IRanges XVector GenomeInfoDb Biostrings curl httr Rsamtools GenomicAlignments BiocIO tools restfulr mgsub: SpatialDatasets: ExperimentHub SpatialExperiment utils profvis: htmlwidgets rlang vctrs survMisc: survival graphics grDevices stats utils knitr KMsurv ggplot2 data.table zoo grid gridExtra km.ci xtable futile.options: splots: grid RColorBrewer syuzhet: textshape NLP zoo dtt stats graphics dplyr tidyr rlang oct4: MethylAid: Biobase BiocParallel BiocGenerics ggplot2 grid gridBase grDevices graphics hexbin matrixStats minfi methods RColorBrewer shiny stats SummarizedExperiment utils isoband: grid utils glue: methods gridBase: graphics grid davidTiling: Biobase tilingArray GO.db furrowSeg: EBImage abind dplyr locfit tiff KEGGgraph: methods XML graph utils RCurl Rgraphviz GOSemSim: AnnotationDbi DBI digest GO.db methods rlang R.utils stats utils yulab.utils Rcpp spam: dotCall64 grid methods Rcpp xfun: grDevices stats tools estrogen: rJava: methods TCGAbiolinksGUI.data: blimaTestingData: readBrukerFlexData: orthosData: AnnotationHub BiocFileCache ExperimentHub HDF5Array stringr SummarizedExperiment mathjaxr: paletteer: prismatic rematch2 rlang rstudioapi ProteinGymR: ExperimentHub AnnotationHub bio3d r3dmol ggExtra dplyr forcats ggdist gghalves ggplot2 pals purrr queryup spdl tidyr tidyselect ComplexHeatmap circlize stringr lifecycle rlang htmltools geneplotter: methods Biobase BiocGenerics lattice annotate AnnotationDbi graphics grDevices grid RColorBrewer stats utils LearnBayes: yulab.utils: cli digest fs rlang tools utils keras: generics reticulate tensorflow tfruns magrittr zeallot glue methods R6 rlang pbkrtest: lme4 broom dplyr MASS methods numDeriv Matrix doBy MassSpecWavelet: RUnit: utils methods graphics planet: methods tibble magrittr dplyr goftest: stats hapmapsnp5: ucminf: hapmapsnp6: BSgenome.Hsapiens.NCBI.GRCh38: BSgenome Matrix: methods grDevices graphics grid lattice stats utils Ckmeans.1d.dp: Rcpp Rdpack wheatmap: grid stats colorspace RColorBrewer eoPredData: ExperimentHub tximportData: GIGSEA: Matrix MASS locfdr stats utils h5vcData: lsa: SnowballC EGSEA: Biobase gage AnnotationDbi topGO pathview PADOG GSVA globaltest limma edgeR HTMLUtils hwriter gplots ggplot2 safe stringi parallel stats metap grDevices graphics utils org.Hs.eg.db org.Mm.eg.db org.Rn.eg.db RColorBrewer methods EGSEAdata htmlwidgets plotly DT scanMiR: Biostrings pwalign GenomicRanges IRanges data.table BiocParallel methods GenomeInfoDb S4Vectors ggplot2 stats stringi utils graphics grid seqLogo cowplot RGMQLlib: DonaPLLP2013: EBImage parallel ggwordcloud: ggplot2 grid gridtext Rcpp scales colorspace png ncdf4: lmerTest: lme4 stats methods numDeriv MASS ggplot2 permute: stats tissueTreg: QDNAseq.hg19: QDNAseq BiocParallel: methods stats utils futile.logger parallel snow codetools BH cpp11 TENxBUSData: ExperimentHub AnnotationHub utils BiocGenerics iC10TrainingData: xmlparsedata: signatureSearchData: ExperimentHub utils affy limma Biobase magrittr dplyr R.utils stats rhdf5 ITALICSData: CAMERA: methods Biobase xcms RBGL graph graphics grDevices stats utils Hmisc igraph fourDNData: BiocFileCache HiCExperiment GenomicRanges IRanges S4Vectors utils tools nabor: Rcpp methods RcppEigen BH lsr: graphics grDevices methods stats taxonomizr: RSQLite R.utils data.table curl survivalROC: digest: utils rvest: cli glue httr lifecycle magrittr rlang selectr tibble xml2 tidyselect: cli glue lifecycle rlang vctrs withr aplot: ggfun ggplot2 ggplotify patchwork magrittr methods utils yulab.utils metapod: Rcpp Delaporte: stats parallel RnBeads.rn5: GenomicRanges hgu133acdf: utils AnnotationDbi listenv: labeling: stats graphics GEOquery: methods Biobase readr xml2 dplyr data.table tidyr magrittr limma curl rentrez R.utils stringr SummarizedExperiment S4Vectors rvest httr2 cli: utils spdl: RcppSpdlog waldo: cli diffobj glue methods rlang RNAmodR.Data: ExperimentHub ExperimentHubData utils ChIPXpressData: bigmemory modelr: broom magrittr purrr rlang tibble tidyr tidyselect vctrs httr: curl jsonlite mime openssl R6 RTCGA.PANCAN12: RTCGA octad.db: ExperimentHub lobstr: crayon methods prettyunits rlang cpp11 XVector: methods BiocGenerics S4Vectors IRanges utils tools lambda.r: formatR emmeans: estimability graphics methods mvtnorm numDeriv stats utils ggtext: ggplot2 grid gridtext rlang scales qvalue: splines ggplot2 grid reshape2 blme: lme4 methods stats utils RTCGA.CNV: RTCGA GetoptLong: rjson GlobalOptions methods crayon bladderbatch: Biobase ScaledMatrix: methods Matrix S4Vectors DelayedArray DNAcopy: rcmdcheck: callr cli curl desc digest pkgbuild prettyunits R6 rprojroot sessioninfo utils withr xopen fission: SummarizedExperiment bsseqData: bsseq affycompData: methods Biobase affycomp ListerEtAlBSseq: methylPipe emtdata: edgeR ExperimentHub SummarizedExperiment selectr: methods stringr R6 BiocManager: utils rcellminer: Biobase rcellminerData stringr gplots ggplot2 methods stats utils shiny OrgMassSpecR: grid bumphunter: S4Vectors IRanges GenomeInfoDb GenomicRanges foreach iterators methods parallel locfit matrixStats limma doRNG BiocGenerics utils GenomicFeatures AnnotationDbi stats sparsevctrs: cli rlang vctrs alabaster.ranges: GenomicRanges alabaster.base methods S4Vectors BiocGenerics IRanges GenomeInfoDb rhdf5 BiocGenerics: methods utils graphics stats generics gdsfmt: methods pkgload: cli desc fs glue lifecycle methods pkgbuild processx rlang rprojroot utils withr MetaGxBreast: Biobase AnnotationHub ExperimentHub stats lattice impute SummarizedExperiment spatialLIBD: SpatialExperiment shiny golem ggplot2 cowplot plotly viridisLite shinyWidgets sessioninfo grid grDevices methods AnnotationHub utils png scater DT ExperimentHub SummarizedExperiment stats graphics S4Vectors IRanges benchmarkme SingleCellExperiment BiocFileCache jsonlite tibble rtracklayer Matrix BiocGenerics GenomicRanges magick paletteer scuttle edgeR limma statmod MatrixGenerics rlang dplyr ComplexHeatmap circlize AssessORF: DECIPHER Biostrings GenomicRanges IRanges graphics grDevices methods stats utils RcppHNSW: methods Rcpp maqcExpression4plex: dir.expiry: utils filelock visNetwork: htmlwidgets htmltools jsonlite magrittr utils methods grDevices stats FlowSorted.CordBlood.450k: minfi sctransform: dplyr magrittr MASS Matrix methods future.apply future ggplot2 reshape2 rlang gridExtra matrixStats RcppArmadillo Rcpp Cairo: grDevices graphics 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 synapterdata: synapter utils RefManageR: xml2 jsonlite utils plyr tools httr lubridate stringr methods bibtex blob: methods rlang vctrs sfheaders: Rcpp geometries PtH2O2lipids: xcms CAMERA LOBSTAHS methods utils EBImage: methods BiocGenerics graphics grDevices stats abind tiff jpeg png locfit fftwtools utils htmltools htmlwidgets RCurl ath1121501cdf: utils AnnotationDbi IHW: methods slam lpsymphony fdrtool BiocGenerics microbenchmark: graphics stats RhpcBLASctl: RcppML: Rcpp Matrix methods stats RcppEigen diagram: shape stats graphics ComplexHeatmap: methods grid graphics stats grDevices circlize GetoptLong colorspace clue RColorBrewer GlobalOptions png digest IRanges matrixStats foreach doParallel codetools GIGSEAdata: MEDIPSData: OMICsPCAdata: MultiAssayExperiment DECIPHER: Biostrings stats methods DBI S4Vectors IRanges XVector vipor: stats graphics class: stats utils MASS frmaTools: affy Biobase DBI methods preprocessCore stats utils AIMS: e1071 Biobase sass: fs rlang htmltools R6 rappdirs beanplot: leidenbase: igraph TxDb.Hsapiens.UCSC.hg19.knownGene: GenomicFeatures AnnotationDbi preprocessCore: stats tfautograph: reticulate backports MethylAidData: MethylAid RTCGA: XML RCurl assertthat stringi rvest data.table xml2 dplyr purrr survival survminer ggplot2 ggthemes viridis knitr scales rmarkdown htmltools Fletcher2013a: limma Biobase VennDiagram gplots grid MACSdata: STexampleData: ExperimentHub SingleCellExperiment SpatialExperiment utils HiContactsData: ExperimentHub BiocFileCache AnnotationHub mia: MultiAssayExperiment SingleCellExperiment SummarizedExperiment TreeSummarizedExperiment ape BiocGenerics BiocParallel Biostrings bluster DECIPHER decontam DelayedArray DelayedMatrixStats DirichletMultinomial dplyr IRanges MASS MatrixGenerics methods rbiom rlang S4Vectors scater scuttle stats stringr tibble tidyr utils vegan Rcpp puma: oligo graphics grDevices methods stats utils mclust oligoClasses Biobase affy affyio rematch2: tibble Fletcher2013b: Fletcher2013a RTN RedeR igraph RColorBrewer restfulr: methods XML RCurl rjson S4Vectors yaml operator.tools: utils SuppDists: splines: graphics stats HiCExperiment: InteractionSet strawr GenomeInfoDb GenomicRanges IRanges S4Vectors BiocGenerics BiocIO BiocParallel methods rhdf5 Matrix vroom dplyr stats biomaRt: methods utils AnnotationDbi progress stringr httr2 digest BiocFileCache rappdirs xml2 curl grid: grDevices utils future.apply: future globals parallel utils infotheo: affyio: methods umap: Matrix methods openssl reticulate Rcpp RSpectra stats TargetScoreData: TENxVisiumData: ExperimentHub SpatialExperiment utils gDRtestData: checkmate data.table NanoporeRNASeq: ExperimentHub gridExtra: gtable grid grDevices graphics utils yeastGSData: RITANdata: bcellViper: Biobase methods hgu95a.db: methods AnnotationDbi org.Hs.eg.db ggvis: assertthat dplyr htmltools jsonlite magrittr methods rlang shiny askpass: sys gaschYHS: Biobase graphics: grDevices hms: lifecycle methods pkgconfig rlang vctrs beachmat: methods DelayedArray SparseArray BiocGenerics Matrix Rcpp assorthead ff: bit utils rex: lazyeval RcppAnnoy: methods Rcpp tilingArray: Biobase methods pixmap strucchange affy vsn genefilter RColorBrewer grid stats4 spatial: graphics stats utils spatstat.random: spatstat.data spatstat.univar spatstat.geom stats utils methods grDevices spatstat.utils RTN: methods RedeR minet viper mixtools snow stats limma data.table IRanges igraph S4Vectors SummarizedExperiment car pwr pheatmap grDevices graphics utils Spectra: S4Vectors BiocParallel ProtGenerics methods IRanges MsCoreUtils graphics grDevices stats tools utils fs BiocGenerics MetaboCoreUtils SPIA: graphics KEGGgraph MicrobiomeBenchmarkData: SummarizedExperiment TreeSummarizedExperiment BiocFileCache tools S4Vectors ape utils diffloopdata: AnnotationFilter: utils methods GenomicRanges lazyeval preciseTADhub: ExperimentHub affxparser: MsCoreUtils: methods S4Vectors MASS stats clue Rcpp fs: methods GenomicAlignments: methods BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges SummarizedExperiment Biostrings Rsamtools utils stats BiocParallel imcdatasets: SingleCellExperiment SpatialExperiment cytomapper methods utils ExperimentHub S4Vectors DelayedArray HDF5Array systemfonts: base64enc grid jsonlite lifecycle tools utils cpp11 MAQCsubset: affy Biobase lumi methods gh: cli gitcreds glue httr2 ini jsonlite lifecycle rlang processx: ps R6 utils Rdpack: methods tools utils rbibutils rgl: graphics grDevices stats utils htmlwidgets htmltools knitr jsonlite magrittr R6 base64enc mime parallel: tools compiler chron: graphics stats vsn: methods Biobase affy limma lattice ggplot2 wesanderson: R.oo: R.methodsS3 methods utils pheatmap: grid RColorBrewer scales gtable stats grDevices graphics TENxPBMCData: SingleCellExperiment HDF5Array AnnotationHub ExperimentHub chromstaRData: prebsdata: TransOmicsData: S4Vectors utils muleaData: RColorBrewer: rngtools: methods digest utils stats parallel MLInterfaces: Rcpp methods BiocGenerics Biobase annotate cluster gdata pls sfsmisc MASS rpart genefilter fpc ggvis shiny gbm RColorBrewer hwriter threejs mlbench stats4 tools grDevices graphics stats magrittr SummarizedExperiment dyebias: marray Biobase ggeffects: graphics insight datawizard stats utils mixOmics: MASS lattice ggplot2 igraph ellipse corpcor RColorBrewer parallel dplyr tidyr reshape2 methods matrixStats rARPACK gridExtra grDevices graphics stats ggrepel BiocParallel utils gsignal rgl PWMEnrich.Mmusculus.background: methods PWMEnrich scatterplot3d: grDevices graphics stats IlluminaHumanMethylation450kmanifest: minfi AnnotationForge: methods utils BiocGenerics Biobase AnnotationDbi DBI RSQLite XML S4Vectors RCurl TxDb.Rnorvegicus.UCSC.rn6.refGene: GenomicFeatures AnnotationDbi MetaScope: BiocFileCache Biostrings data.table dplyr ggplot2 magrittr Matrix MultiAssayExperiment Rbowtie2 readr rlang Rsamtools S4Vectors stringr SummarizedExperiment taxonomizr tibble tidyr tools mlbench: mapproj: maps stats graphics CGHcall: impute DNAcopy methods Biobase CGHbase snowfall litedown: utils commonmark xfun queryup: httr jsonlite utils TENxBrainData: SingleCellExperiment HDF5Array AnnotationHub ExperimentHub JohnsonKinaseData: ExperimentHub BiocParallel checkmate dplyr stats stringr tidyr purrr utils frmaExampleData: pracma: graphics grDevices stats utils sampleClassifierData: SummarizedExperiment ProData: Biobase AzureRMR: AzureGraph AzureAuth utils parallel httr jsonlite R6 uuid jquerylib: htmltools whisker: nloptr: prabclus: MASS mclust classInt: grDevices stats graphics e1071 class KernSmooth SpikeInSubset: Biobase affy dendsort: spatialreg: spData Matrix sf spdep coda methods MASS boot splines LearnBayes nlme multcomp foreach: codetools utils iterators parallelly: parallel tools utils FlowSorted.DLPFC.450k: minfi profileModel: slam: stats mvtnorm: stats iC10: pamr impute iC10TrainingData ARRmData: cnvGSAdata: cnvGSA CONFESSdata: scater: SingleCellExperiment scuttle ggplot2 stats utils methods Matrix BiocGenerics S4Vectors SummarizedExperiment MatrixGenerics SparseArray DelayedArray beachmat BiocNeighbors BiocSingular BiocParallel rlang ggbeeswarm viridis Rtsne RColorBrewer RcppML uwot pheatmap ggrepel ggrastr magrittr: logger: utils GenomicFeatures: BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges AnnotationDbi methods utils stats DBI XVector Biostrings rtracklayer fastDummies: data.table tibble stringr rintrojs: shiny jsonlite tuberculosis: SummarizedExperiment AnnotationHub ExperimentHub S4Vectors dplyr magrittr purrr rlang stringr tibble tidyr base64enc: dynamicTreeCut: stats randomForest: stats tsne: estimability: stats Gviz: methods S4Vectors IRanges GenomicRanges grid XVector rtracklayer lattice RColorBrewer biomaRt AnnotationDbi Biobase GenomicFeatures ensembldb BSgenome Biostrings biovizBase Rsamtools latticeExtra matrixStats GenomicAlignments GenomeInfoDb BiocGenerics digest graphics grDevices stats utils norm: stats NLP: utils ReactomeGSA.data: limma edgeR ReactomeGSA Seurat PREDAsampledata: methods PREDA Biobase affy annotate pasilla: DEXSeq kableExtra: knitr magrittr stringr xml2 rmarkdown scales viridisLite stats grDevices htmltools rstudioapi tools digest graphics svglite ica: adductData: ExperimentHub AnnotationHub stats utils methods datasets covr: methods digest stats utils jsonlite rex httr crayon withr yaml ggrastr: ggplot2 Cairo ggbeeswarm grid png ragg UpSetR: ggplot2 gridExtra plyr utils stats methods grDevices scales gghalves: ggplot2 grid gtable grDevices MetaGxPancreas: SummarizedExperiment ExperimentHub stats impute S4Vectors AnnotationHub stabledist: stats modeest: fBasics stable stabledist stats statip MultiAssayExperiment: SummarizedExperiment Biobase BiocBaseUtils BiocGenerics DelayedArray GenomicRanges IRanges methods S4Vectors tidyr utils bio3d: Rcpp parallel grid graphics grDevices stats utils assorthead: viridisLite: hunspell: Rcpp digest vroom: bit64 cli crayon glue hms lifecycle methods rlang stats tibble tidyselect tzdb vctrs withr cpp11 progress AnnotationHubData: methods utils S4Vectors IRanges GenomicRanges AnnotationHub GenomicFeatures Rsamtools rtracklayer BiocGenerics jsonlite BiocManager biocViews BiocCheck graph AnnotationDbi Biobase Biostrings DBI GenomeInfoDb OrganismDbi RSQLite AnnotationForge futile.logger XML RCurl DExMAdata: Biobase GenomicDistributionsData: ExperimentHub AnnotationHub AnnotationFilter data.table utils BSgenome GenomeInfoDb GenomicFeatures GenomicRanges ensembldb healthyFlowData: flowCore methods CoSIAdata: ExperimentHub illuminaHumanv2.db: methods AnnotationDbi org.Hs.eg.db 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 hwriter: ConsensusClusterPlus: Biobase ALL graphics stats utils cluster shinyjs: digest jsonlite shiny rlist: yaml jsonlite XML data.table humanHippocampus2024: ExperimentHub SummarizedExperiment SpatialExperiment gargle: cli fs glue httr jsonlite lifecycle openssl rappdirs rlang stats utils withr lattice: grid grDevices graphics stats utils ChIPexoQualExample: BloodCancerMultiOmics2017: beeswarm Biobase DESeq2 devtools dplyr ggdendro ggplot2 glmnet graphics grDevices grid gtable ipflasso methods RColorBrewer reshape2 scales stats SummarizedExperiment survival tibble flexmix: lattice graphics grid grDevices methods modeltools nnet stats stats4 utils kidpack: Biobase MerfishData: EBImage SpatialExperiment grDevices AnnotationHub BumpyMatrix ExperimentHub S4Vectors SingleCellExperiment SummarizedExperiment HDF5Array MatrixModels: stats methods Matrix ids: openssl uuid gplots: gtools stats caTools KernSmooth methods LRcellTypeMarkers: ExperimentHub mixtools: kernlab MASS plotly scales segmented stats survival fields: methods spam viridisLite maps simpIntLists: oligoClasses: BiocGenerics Biobase methods graphics IRanges GenomicRanges SummarizedExperiment Biostrings affyio foreach BiocManager utils S4Vectors RSQLite DBI ff rheumaticConditionWOLLBOLD: data.tree: R6 stringi methods scrime: methods stats utils ggforce: ggplot2 grid scales MASS tweenr gtable rlang polyclip stats grDevices tidyselect withr utils lifecycle cli vctrs systemfonts cpp11 nor1mix: stats graphics IlluminaHumanMethylationEPICanno.ilm10b4.hg19: minfi yaml: fdrtool: graphics grDevices stats rmutil: hexbin: methods lattice grid graphics grDevices stats utils sitmo: Rcpp depmap: methods dplyr utils ExperimentHub AnnotationHub BiocFileCache httr2 curl tibble metap: lattice Rdpack TFisher mutoss mathjaxr qqconf spqnData: SummarizedExperiment DEXSeq: BiocParallel Biobase SummarizedExperiment IRanges GenomicRanges DESeq2 AnnotationDbi RColorBrewer S4Vectors BiocGenerics biomaRt hwriter methods stringr Rsamtools statmod geneplotter genefilter SomatiCAData: gower: survminer: ggplot2 ggpubr grid gridExtra magrittr maxstat methods scales survival stats broom dplyr tidyr survMisc purrr tibble rlang ggtext org.Dm.eg.db: methods AnnotationDbi pdInfoBuilder: methods Biobase RSQLite affxparser oligo Biostrings BiocGenerics DBI IRanges oligoClasses S4Vectors koRpus: sylly data.table methods Matrix Hiiragi2013: KEGGREST affy boot clue genefilter geneplotter gtools mouse4302.db xtable MASS Biobase RColorBrewer cluster gplots grid lattice latticeExtra BeadArrayUseCases: beadarray limma GEOquery ShortRead: BiocGenerics BiocParallel Biostrings Rsamtools GenomicAlignments Biobase S4Vectors IRanges GenomeInfoDb GenomicRanges pwalign hwriter methods lattice latticeExtra XVector Rhtslib TBX20BamSubset: Rsamtools xtable HiCDataLymphoblast: nat: rgl nabor igraph methods filehash digest nat.utils plyr yaml abind: methods utils robustbase: stats graphics utils methods DEoptimR Deriv: methods brew: ordinal: stats methods ucminf MASS Matrix numDeriv nlme snowfall: snow MALDIquantForeign: methods MALDIquant base64enc digest readBrukerFlexData readMzXmlData XML curatedPCaData: S4Vectors MultiAssayExperiment RaggedExperiment ExperimentHub AnnotationHub utils methods rlang stats reshape2 ASICSdata: scpdata: QFeatures ExperimentHub utils AnnotationHub SingleCellExperiment S4Vectors gdtools: fontquiver htmltools Rcpp systemfonts tools rappdirs: bit64: bit graphics methods stats utils xgboost: Matrix methods data.table jsonlite lubridate: methods generics timechange gDRstyle: BiocCheck BiocManager BiocStyle checkmate desc git2r lintr rcmdcheck remotes yaml rjson pkgbuild withr logistf: mice mgcv formula.tools Matrix squash: graphics grDevices methods stats TCGAMethylation450k: msm: survival mvtnorm expm generics tibble BiocIO: BiocGenerics S4Vectors methods tools celarefData: s2: Rcpp wk txdbmaker: BiocGenerics S4Vectors GenomeInfoDb GenomicRanges GenomicFeatures methods utils stats tools httr rjson DBI RSQLite IRanges UCSC.utils AnnotationDbi Biobase BiocIO rtracklayer biomaRt DAPAR: Biobase MSnbase DAPARdata utils highcharter foreach SRAdb: RSQLite graph RCurl R.utils zeallot: downlit: brio desc digest evaluate fansi memoise rlang vctrs withr yaml enviPat: xtable: stats utils microRNAome: SummarizedExperiment ggside: ggplot2 grid gtable rlang scales cli glue stats tibble vctrs hapmap500ksty: latticeExtra: lattice grid stats utils grDevices png jpeg RColorBrewer interp MASS HarmanData: seventyGeneData: hgu133plus2.db: methods AnnotationDbi org.Hs.eg.db cytomapper: EBImage SingleCellExperiment methods SpatialExperiment S4Vectors BiocParallel HDF5Array DelayedArray RColorBrewer viridis utils SummarizedExperiment tools graphics raster grDevices stats ggplot2 ggbeeswarm svgPanZoom svglite shiny shinydashboard matrixStats rhdf5 nnls clustifyrdatahub: ExperimentHub utils callr: processx R6 utils sourcetools: ps: utils bitops: generics: methods tools: exactRankTests: stats utils RSQLite: bit64 blob DBI memoise methods pkgconfig rlang plogr cpp11 logging: methods rpx: methods BiocFileCache jsonlite xml2 RCurl curl utils KernSmooth: stats ggplotify: ggplot2 graphics grDevices grid gridGraphics yulab.utils yeastNagalakshmi: rentrez: XML httr jsonlite brio: treeio: ape dplyr jsonlite magrittr methods rlang stats tibble tidytree utils yulab.utils cfToolsData: utils ExperimentHub DAPARdata: MSnbase utils terra: methods Rcpp TMExplorer: SingleCellExperiment BiocFileCache methods Matrix MMDiff2: Rsamtools Biobase GenomicRanges locfit BSgenome Biostrings shiny ggplot2 RColorBrewer graphics grDevices parallel S4Vectors methods DESeq2: S4Vectors IRanges GenomicRanges SummarizedExperiment BiocGenerics Biobase BiocParallel matrixStats methods stats4 locfit ggplot2 Rcpp MatrixGenerics RcppArmadillo filesstrings: stringr checkmate magrittr purrr rlang strex stringi withr qs: Rcpp RApiSerialize stringfish BH hgu133plus2barcodevecs: mitools: DBI methods stats graphlayouts: igraph Rcpp RcppArmadillo xcms: BiocParallel MSnbase mzR methods Biobase BiocGenerics ProtGenerics lattice MassSpecWavelet S4Vectors IRanges SummarizedExperiment MsCoreUtils MsFeatures MsExperiment Spectra progress RColorBrewer MetaboCoreUtils spatstat.explore: spatstat.data spatstat.univar spatstat.geom spatstat.random stats graphics grDevices utils methods nlme spatstat.utils spatstat.sparse goftest Matrix abind httpuv: later promises R6 Rcpp utils alabaster.matrix: alabaster.base methods BiocGenerics S4Vectors DelayedArray S4Arrays SparseArray rhdf5 HDF5Array Matrix Rcpp marray: limma methods koRpus.lang.en: koRpus methods sylly.en hapmap100kxba: curatedBreastData: XML ggplot2 impute Biobase BiocStyle methods stats DNAZooData: HiCExperiment BiocFileCache S4Vectors rjson utils tools pcaMethods: Biobase methods BiocGenerics Rcpp MASS BatchJobs: BBmisc methods backports brew checkmate data.table DBI digest parallel RSQLite sendmailR stats stringi utils ggstats: cli dplyr forcats ggplot2 lifecycle patchwork purrr rlang scales stats stringr utils tidyr nortest: stats sf: methods classInt DBI graphics grDevices grid magrittr s2 stats tools units utils Rcpp XhybCasneuf: affy ath1121501cdf tinesath1cdf RColorBrewer methods grid SparseArray: methods Matrix BiocGenerics MatrixGenerics S4Vectors S4Arrays utils stats matrixStats IRanges XVector XML: methods utils survival: graphics Matrix methods splines stats utils broom: backports cli dplyr generics glue lifecycle purrr rlang stringr tibble tidyr svgPanZoom: htmlwidgets sn: methods stats4 mnormt numDeriv utils quantreg sp: methods utils stats graphics grDevices lattice grid scp: QFeatures IHW ggplot2 ggrepel matrixStats metapod methods MsCoreUtils MultiAssayExperiment nipals RColorBrewer S4Vectors SingleCellExperiment SummarizedExperiment stats utils spData: sp zebrafishRNASeq: MethylSeqData: SummarizedExperiment ExperimentHub HDF5Array rhdf5 GenomeInfoDb S4Vectors GenomicRanges stats IRanges utils TargetSearchData: cleaver: methods Biostrings S4Vectors IRanges mtbls2: matrixStats: fftwtools: enrichplot: aplot DOSE ggfun ggnewscale ggplot2 ggrepel ggtangle graphics grid igraph methods plyr purrr RColorBrewer reshape2 rlang stats utils scatterpie GOSemSim magrittr ggtree yulab.utils multtest: methods BiocGenerics Biobase survival MASS stats4 deSolve: methods graphics grDevices stats benchmarkme: benchmarkmeData compiler doParallel dplyr foreach graphics httr Matrix methods parallel stringr tibble utils TxDb.Rnorvegicus.UCSC.rn5.refGene: GenomicFeatures AnnotationDbi qpdf: Rcpp askpass curl ggsignif: ggplot2 spelling: commonmark xml2 hunspell knitr AzureGraph: AzureAuth utils httr jsonlite openssl curl R6 LRcell: ExperimentHub AnnotationHub BiocParallel dplyr ggplot2 ggrepel magrittr stats utils tm: NLP Rcpp parallel slam stats tools utils graphics xml2 BH CLLmethylation: SummarizedExperiment ExperimentHub markdown: utils xfun litedown hapmap500knsp: Rcpp: methods utils ffpeExampleData: lumi DMRcatedata: ExperimentHub GenomicFeatures Gviz readxl plyr rtracklayer IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylationEPICanno.ilm10b4.hg19 scaeData: ExperimentHub MEEBOdata: msmsEDA: MSnbase MASS gplots RColorBrewer qPLEXdata: qPLEXanalyzer utils knitr MSnbase dplyr mzR: Rcpp methods utils Biobase BiocGenerics ProtGenerics ncdf4 Rhdf5lib xml2: cli methods rlang formatR: ensembldb: BiocGenerics GenomicRanges GenomicFeatures AnnotationFilter methods RSQLite DBI Biobase GenomeInfoDb AnnotationDbi rtracklayer S4Vectors Rsamtools IRanges ProtGenerics Biostrings curl pROC: methods plyr Rcpp hgu133plus2frmavecs: Signac: methods GenomeInfoDb GenomicRanges IRanges Matrix Rsamtools S4Vectors SeuratObject data.table dplyr future future.apply ggplot2 rlang irlba pbapply tidyr patchwork stats utils BiocGenerics stringi fastmatch RcppRoll scales Rcpp grid tidyselect vctrs lifecycle scds: Matrix S4Vectors SingleCellExperiment SummarizedExperiment xgboost methods stats dplyr pROC animalcules: ape assertthat caret covr DESeq2 dplyr DT forcats ggforce ggplot2 GUniFrac lattice limma magrittr Matrix methods MultiAssayExperiment plotly rentrez reshape2 ROCit S4Vectors scales shiny shinyjs stats SummarizedExperiment tibble tidyr tsne umap utils vegan XML ipred: rpart MASS survival nnet class prodlim GSE62944: Biobase GEOquery TxDb.Rnorvegicus.UCSC.rn4.ensGene: GenomicFeatures AnnotationDbi jsonlite: methods tensorflow: config processx reticulate tfruns utils yaml grDevices tfautograph rstudioapi lifecycle breastCancerNKI: FlowSorted.Blood.450k: minfi prostateCancerStockholm: Biobase spdep: methods spData sf stats deldir boot graphics utils grDevices units s2 e1071 sp metaMSdata: flowWorkspaceData: BiSeq: methods S4Vectors IRanges GenomicRanges SummarizedExperiment Formula BiocGenerics Biobase GenomeInfoDb rtracklayer parallel betareg lokern globaltest BeadDataPackR: stats utils GWASTools: Biobase graphics stats utils methods gdsfmt DBI RSQLite GWASExactHW 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multtest splines methods stats4 grDevices graphics stats scrime shinyWidgets: bslib sass shiny htmltools jsonlite grDevices rlang SnowballC: tidytext: cli dplyr generics janeaustenr lifecycle Matrix methods purrr rlang stringr tibble tokenizers vctrs MSnID: Rcpp MSnbase mzID R.cache foreach doParallel parallel methods iterators data.table Biobase ProtGenerics reshape2 dplyr mzR BiocStyle msmsTests ggplot2 RUnit BiocGenerics Biostrings purrr rlang stringr tibble AnnotationHub AnnotationDbi xtable mice: broom dplyr glmnet graphics grDevices lattice mitml nnet Rcpp rpart stats tidyr utils cpp11 htmlTable: stringr knitr magrittr methods checkmate htmlwidgets htmltools rstudioapi flowCore: Biobase BiocGenerics grDevices graphics methods stats utils stats4 Rcpp matrixStats cytolib S4Vectors cpp11 BH RProtoBufLib MouseThymusAgeing: SingleCellExperiment SummarizedExperiment ExperimentHub methods BiocGenerics S4Vectors RnBeads.hg38: GenomicRanges affy: BiocGenerics Biobase affyio BiocManager graphics grDevices methods preprocessCore stats utils entropy: wk: magick: Rcpp magrittr curl RegParallel: doParallel foreach parallel iterators data.table stringr survival arm stats utils methods decontam: methods ggplot2 reshape2 stats textstem: koRpus.lang.en dplyr hunspell koRpus lexicon quanteda SnowballC stats stringi textclean textshape utils oligo: BiocGenerics oligoClasses Biobase Biostrings affyio affxparser DBI ff graphics methods preprocessCore RSQLite splines stats stats4 utils bit optimalFlowData: SingleMoleculeFootprintingData: ExperimentHub utils ExperimentHubData: utils BiocGenerics S4Vectors AnnotationHubData methods ExperimentHub BiocManager DBI httr curl getDEE2: stats utils SummarizedExperiment htm2txt extrafont: extrafontdb grDevices utils Rttf2pt1 parathyroidSE: SummarizedExperiment colorspace: methods graphics grDevices stats TxDb.Hsapiens.UCSC.hg38.knownGene: GenomicFeatures AnnotationDbi GSE159526: ggraph: ggplot2 dplyr ggforce grid igraph scales MASS ggrepel utils stats viridis rlang tidygraph graphlayouts withr cli vctrs lifecycle memoise cpp11 bigmemory.sri: methods bigmemory: bigmemory.sri methods utils Rcpp uuid BH breastCancerMAINZ: rmarkdown: bslib evaluate fontawesome htmltools jquerylib jsonlite knitr methods tinytex tools utils xfun yaml pwalign: BiocGenerics S4Vectors IRanges Biostrings methods utils XVector HighlyReplicatedRNASeq: SummarizedExperiment ExperimentHub S4Vectors mvoutData: methods Biobase affy lumi EatonEtAlChIPseq: GenomicRanges ShortRead rtracklayer EnrichmentBrowser: SummarizedExperiment graph AnnotationDbi BiocFileCache BiocManager GSEABase GO.db KEGGREST KEGGgraph Rgraphviz S4Vectors SPIA edgeR graphite hwriter limma methods pathview safe progressr: digest utils cellranger: rematch tibble timeSeries: timeDate methods graphics grDevices stats utils dyebiasexamples: marray GEOquery stats: utils grDevices graphics dtt: lpSolve: tartare: AnnotationHub ExperimentHub utils RnBeads.mm9: GenomicRanges RnBeads.hg19: GenomicRanges DLBCL: Biobase graph faahKO: xcms bsseq: methods BiocGenerics GenomicRanges SummarizedExperiment IRanges GenomeInfoDb scales stats parallel tools graphics Biobase locfit gtools data.table S4Vectors R.utils DelayedMatrixStats permute limma DelayedArray Rcpp BiocParallel BSgenome Biostrings utils HDF5Array rhdf5 beachmat assorthead grndata: GEOmetadb: R.utils RSQLite Rbowtie2: magrittr Rsamtools plyr: Rcpp MatrixGenerics: matrixStats methods FieldEffectCrc: utils BiocStyle RUnit SummarizedExperiment ExperimentHub AnnotationHub DESeq2 colorRamps: muscat: BiocParallel blme ComplexHeatmap data.table DESeq2 dplyr edgeR ggplot2 glmmTMB grDevices grid limma lmerTest lme4 Matrix matrixStats methods progress purrr rlang S4Vectors scales scater scuttle sctransform stats SingleCellExperiment SummarizedExperiment variancePartition viridis bodymapRat: SummarizedExperiment ExperimentHub utils SummarizedExperiment: methods MatrixGenerics GenomicRanges Biobase utils stats tools Matrix BiocGenerics S4Vectors IRanges GenomeInfoDb S4Arrays DelayedArray pepDat: GenomicRanges TxDb.Mmusculus.UCSC.mm9.knownGene: GenomicFeatures AnnotationDbi PSMatch: S4Vectors utils stats igraph methods Spectra Matrix BiocParallel BiocGenerics ProtGenerics QFeatures MsCoreUtils IRanges HD2013SGI: RColorBrewer gplots geneplotter splots limma vcd LSD EBImage curl: sylly.en: sylly lokern: grDevices graphics stats utils sfsmisc RTCGA.mRNA: RTCGA VectraPolarisData: ExperimentHub SpatialExperiment utils timecoursedata: SummarizedExperiment TabulaMurisData: ExperimentHub utils mammaPrintData: sparseMatrixStats: MatrixGenerics Rcpp Matrix matrixStats methods desc: cli R6 utils OnassisJavaLibs: rJava msmsTests: MSnbase msmsEDA edgeR qvalue ggspavis: ggplot2 SpatialExperiment SingleCellExperiment SummarizedExperiment ggside grid ggrepel RColorBrewer scales grDevices methods stats ggridges: ggplot2 grid scales withr rversions: curl utils xml2 dirmult: assertthat: tools lifecycle: cli glue rlang ggsci: ggplot2 grDevices scales dressCheck: methods Biobase survcomp: survival prodlim ipred SuppDists KernSmooth survivalROC bootstrap grid rmeta stats graphics M3DExampleData: Rttf2pt1: ccdata: NxtIRFdata: ExperimentHub BiocFileCache rtracklayer R.utils Formula: stats urlchecker: cli curl tools xml2 Affyhgu133Plus2Expr: extrafontdb: GO.db: methods AnnotationDbi DeSousa2013: affy frma frmaTools hgu133plus2.db hgu133plus2frmavecs sva rgl ConsensusClusterPlus cluster siggenes ROCR pamr survival gplots AnnotationDbi Biobase R.utils: R.oo methods utils tools R.methodsS3 flashClust: hapmap100khind: uwot: Matrix FNN irlba methods Rcpp RcppAnnoy RSpectra dqrng RcppProgress TxDb.Dmelanogaster.UCSC.dm3.ensGene: GenomicFeatures AnnotationDbi jsonvalidate: R6 V8 PolynomF: graphics grDevices stats Rcpp methods doRNG: foreach rngtools stats utils iterators latex2exp: stringr magrittr affycomp: methods Biobase polyclip: AshkenazimSonChr21: HMP2Data: AnnotationHub assertthat dplyr ExperimentHub kableExtra knitr magrittr methods readr S4Vectors SummarizedExperiment phyloseq MultiAssayExperiment data.table Affyhgu133aExpr: org.Rn.eg.db: methods AnnotationDbi dichromat: stats breastCancerUNT: alabaster.base: alabaster.schemas methods utils S4Vectors rhdf5 jsonlite jsonvalidate Rcpp assorthead Rhdf5lib english: quantsmooth: quantreg grid plotrix: grDevices graphics stats utils sylly: methods protViz: methods Rcpp signal: MASS graphics grDevices stats utils ASSIGN: gplots graphics grDevices msm Rlab stats sva utils ggplot2 yaml 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 statip: clue graphics rpart stats harbChIP: tools utils IRanges Biobase Biostrings methods stats topdownrdata: topdownr ptairData: rhdf5 signal stats graphics SVM2CRMdata: tweeDEseqCountData: Biobase CellMapperData: ExperimentHub CellMapper xcoredata: ExperimentHub utils IRanges: methods utils stats BiocGenerics S4Vectors stats4 MsFeatures: methods ProtGenerics MsCoreUtils SummarizedExperiment stats leukemiasEset: Biobase caret: ggplot2 lattice e1071 foreach grDevices methods ModelMetrics nlme plyr pROC recipes reshape2 stats stats4 utils withr nleqslv: rlang: utils GSBenchMark: ALL: Biobase webchem: xml2 httr rvest jsonlite stringr methods dplyr purrr data.tree tibble base64enc rlang utils COHCAPanno: KEGGandMetacoreDzPathwaysGEO: Biobase BiocGenerics curatedAdipoChIP: SummarizedExperiment ExperimentHub tensorA: stats multiWGCNA: ggalluvial stringr readr WGCNA dplyr reshape2 data.table patchwork scales igraph flashClust ggplot2 dcanr cowplot ggrepel methods SummarizedExperiment rRDPData: rRDP colonCA: Biobase EpipwR.data: ExperimentHub TMB: graphics methods stats utils Matrix RcppEigen httr2: cli curl glue lifecycle magrittr openssl R6 rappdirs rlang vctrs withr ggplot2: cli glue grDevices grid gtable isoband lifecycle MASS mgcv rlang scales stats tibble vctrs withr BBmisc: checkmate data.table methods stats 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 caTools: bitops rhdf5: methods Rhdf5lib rhdf5filters bambu: SummarizedExperiment S4Vectors BSgenome IRanges BiocGenerics BiocParallel data.table dplyr tidyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges stats Rsamtools methods Rcpp xgboost RcppArmadillo Biobase: BiocGenerics utils methods RApiSerialize: numDeriv: sampling: MASS lpSolve quadprog: fansi: grDevices utils BiocCheck: BiocBaseUtils BiocFileCache BiocManager biocViews callr cli codetools graph httr2 knitr methods rvest stringdist tools utils rbiom: methods mgcv stats utils ape dplyr emmeans fillpattern ggbeeswarm ggnewscale ggplot2 ggrepel ggtext jsonlite magrittr parallelly patchwork pillar plyr readr readxl slam vegan ChAMPdata: GenomicRanges BiocGenerics PepsNMRData: EpiMix.data: ExperimentHub epimutacionsData: muscData: ExperimentHub SingleCellExperiment utils compiler: topdownr: methods BiocGenerics ProtGenerics Biostrings S4Vectors grDevices stats tools utils Biobase Matrix MSnbase PSMatch ggplot2 mzR ISOcodes: Rsamtools: methods GenomeInfoDb GenomicRanges Biostrings utils BiocGenerics S4Vectors IRanges XVector bitops BiocParallel stats Rhtslib aracne.networks: viper RNAseqData.HNRNPC.bam.chr14: miRNATarget: Biobase statmod: stats graphics BiocStyle: bookdown knitr rmarkdown stats utils yaml BiocManager ANF: igraph Biobase survival MASS stats RColorBrewer hgu95av2cdf: utils AnnotationDbi hgu2beta7: qdapRegex: stringi spatialDmelxsim: ExperimentHub SummarizedExperiment utils pkgdown: bslib callr cli desc downlit fontawesome fs httr2 jsonlite openssl purrr ragg rlang rmarkdown tibble whisker withr xml2 yaml limma: grDevices graphics stats utils methods statmod RMassBankData: locfdr: stats splines graphics clustifyr: cowplot dplyr entropy fgsea ggplot2 Matrix rlang scales stringr tibble tidyr stats methods SingleCellExperiment SummarizedExperiment SeuratObject matrixStats S4Vectors proxy httr utils viridis: viridisLite ggplot2 gridExtra iterators: utils metadat: utils tools mathjaxr fibroEset: Biobase nlme: graphics stats utils lattice mime: tools geneLenDataBase: utils rtracklayer GenomicFeatures txdbmaker Neve2006: tools methods utils Biobase hgu133a.db annotate bdsmatrix: methods geepack: methods MASS broom magrittr specL: DBI methods protViz RSQLite seqinr geneExpressionFromGEO: xml2 Biobase annotate GEOquery qpdf curatedOvarianData: Biobase BiocGenerics NGScopyData: corpcor: stats ROCR: methods graphics grDevices gplots stats matter: BiocParallel Matrix methods BiocGenerics ProtGenerics digest irlba stats stats4 graphics grDevices parallel utils BH ChemmineR: methods rjson graphics stats RCurl DBI digest BiocGenerics Rcpp ggplot2 grid gridExtra png base64enc DT rsvg jsonlite stringi BH fastqcr: dplyr grid gridExtra ggplot2 magrittr readr rmarkdown rvest tibble tidyr scales stats utils xml2 rlang FIs: scales: cli farver glue labeling lifecycle R6 RColorBrewer rlang viridisLite FlowSorted.Blood.EPIC: minfi ExperimentHub genefilter nlme quadprog graphics stats utils AnnotationHub SummarizedExperiment S4Vectors backports: UCSC.utils: methods stats httr jsonlite S4Vectors shinyBS: shiny htmltools prettyunits: minfiDataEPIC: minfi IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICanno.ilm10b2.hg19 microbiomeDataSets: SummarizedExperiment TreeSummarizedExperiment MultiAssayExperiment methods utils BiocGenerics ExperimentHub Biostrings ape HiTC: methods IRanges GenomicRanges Biostrings graphics grDevices rtracklayer RColorBrewer Matrix parallel GenomeInfoDb yeastCC: Biobase minet: infotheo segmented: MASS nlme xcore: DelayedArray edgeR foreach GenomicRanges glmnet IRanges iterators magrittr Matrix methods MultiAssayExperiment stats S4Vectors utils minfi: methods BiocGenerics GenomicRanges SummarizedExperiment Biostrings bumphunter S4Vectors GenomeInfoDb Biobase IRanges beanplot RColorBrewer lattice nor1mix siggenes limma preprocessCore illuminaio DelayedMatrixStats mclust genefilter nlme reshape MASS quadprog data.table GEOquery stats grDevices graphics utils DelayedArray HDF5Array BiocParallel ALLMLL: affy QDNAseq.mm10: QDNAseq curatedAdipoRNA: SummarizedExperiment org.Sc.sgd.db: methods AnnotationDbi 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 itertools: iterators parallel RTCGA.mutations: RTCGA Single.mTEC.Transcriptomes: gridtext: curl grid grDevices markdown rlang Rcpp png jpeg stringr xml2 gert: askpass credentials openssl rstudioapi sys zip tidytree: ape dplyr lazyeval magrittr methods rlang tibble tidyr tidyselect yulab.utils pillar cli gage: graph KEGGREST AnnotationDbi GO.db praise: scuttle: SingleCellExperiment methods utils stats Matrix Rcpp BiocGenerics S4Vectors BiocParallel GenomicRanges SummarizedExperiment S4Arrays MatrixGenerics SparseArray DelayedArray beachmat rstudioapi: rjson: Rdisop: Rcpp HiCDataHumanIMR90: quanteda: methods fastmatch jsonlite lifecycle magrittr Matrix Rcpp SnowballC stopwords stringi xml2 yaml GWASdata: GWASTools GSVA: methods stats utils graphics S4Vectors IRanges Biobase SummarizedExperiment GSEABase Matrix parallel BiocParallel SingleCellExperiment SpatialExperiment sparseMatrixStats DelayedArray DelayedMatrixStats HDF5Array BiocSingular cli HelloRangesData: yeastRNASeq: SubcellularSpatialData: dplyr hexbin Matrix SpatialExperiment stats plogr: hgu133a.db: methods AnnotationDbi org.Hs.eg.db tzdb: cpp11 rhdf5filters: Rhdf5lib mutoss: mvtnorm plotrix multtest multcomp methods stats4: graphics methods stats biomformat: methods plyr jsonlite Matrix rhdf5 datawizard: insight stats utils tibble: cli lifecycle magrittr methods pillar pkgconfig rlang utils vctrs pkgconfig: utils readxl: cellranger tibble utils cpp11 progress FNN: MUGAExampleData: PathNetData: fgsea: Rcpp data.table BiocParallel stats ggplot2 cowplot grid fastmatch Matrix scales utils BH synapter: methods MSnbase RColorBrewer lattice qvalue multtest utils tools Biobase Biostrings cleaver readr rmarkdown GenomicFiles: methods BiocGenerics MatrixGenerics GenomicRanges SummarizedExperiment BiocParallel Rsamtools rtracklayer GenomicAlignments IRanges S4Vectors VariantAnnotation GenomeInfoDb leaps: CardinalWorkflows: Cardinal methods etec16s: Biobase metagenomeSeq ggtree: ape aplot dplyr ggplot2 grid magrittr methods purrr rlang ggfun yulab.utils tidyr tidytree treeio utils scales stats cli scatterpie: ggplot2 ggforce rlang ggfun stats tidyr dplyr utils yulab.utils DOSE: AnnotationDbi BiocParallel fgsea ggplot2 GOSemSim methods qvalue reshape2 stats utils yulab.utils scattermore: ggplot2 scales grid grDevices graphics gpaExample: clue: stats cluster graphics methods scMultiome: AnnotationHub ExperimentHub MultiAssayExperiment SingleCellExperiment SummarizedExperiment AzureStor GenomicRanges HDF5Array S4Vectors checkmate methods rhdf5 alabaster.matrix quantreg: stats SparseM methods graphics Matrix MatrixModels survival MASS AzureAuth: utils httr openssl jsonlite jose R6 rappdirs aCGH: cluster survival multtest Biobase grDevices graphics methods stats splines utils plotly: ggplot2 tools scales httr jsonlite magrittr digest viridisLite base64enc htmltools htmlwidgets tidyr RColorBrewer dplyr vctrs tibble lazyeval rlang crosstalk purrr data.table promises cachem: rlang fastmap dbscan: generics graphics Rcpp stats Harman: Rcpp graphics stats Ckmeans.1d.dp parallel methods matrixStats vegan: permute MASS cluster lattice mgcv multcomp: stats graphics mvtnorm survival TH.data sandwich codetools pixmap: methods graphics grDevices 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farver serumStimulation: piano: BiocGenerics Biobase gplots igraph relations marray fgsea shiny DT htmlwidgets shinyjs shinydashboard visNetwork scales grDevices graphics stats utils methods prostateCancerGrasso: Biobase DrugVsDiseasedata: QDNAseq: graphics methods stats utils Biobase CGHbase CGHcall DNAcopy GenomicRanges IRanges matrixStats R.utils Rsamtools future.apply genomationData: pumadata: Biobase puma oligo stemHypoxia: TTR: xts zoo curl remaCor: ggplot2 methods mvtnorm grid reshape2 compiler Rcpp EnvStats Rdpack stats RcppArmadillo org.Mm.eg.db: methods AnnotationDbi IHWpaper: IHW Rcpp stats splines methods utils DESeq2 SummarizedExperiment fdrtool genefilter qvalue Biobase BiocGenerics BiocParallel dplyr grid ggplot2 cowplot gitcreds: DropletUtils: SingleCellExperiment utils stats methods Matrix Rcpp BiocGenerics S4Vectors IRanges GenomicRanges SummarizedExperiment BiocParallel SparseArray DelayedArray DelayedMatrixStats HDF5Array rhdf5 edgeR R.utils dqrng beachmat scuttle 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stats methods BiocGenerics httr multcompView: grid benchmarkfdrData2019: SummarizedExperiment ExperimentHub utils RcppRoll: Rcpp brglm: profileModel RnBeads.mm10: GenomicRanges shinyMethylData: sesameData: ExperimentHub AnnotationHub utils readr stringr GenomicRanges S4Vectors IRanges GenomeInfoDb highr: xfun xts: zoo methods rols: methods httr2 jsonlite utils Biobase BiocGenerics nipals: BiocBaseUtils: methods utils VariantTools: S4Vectors IRanges GenomicRanges VariantAnnotation methods Rsamtools BiocGenerics Biostrings parallel GenomicFeatures Matrix rtracklayer BiocParallel GenomeInfoDb BSgenome Biobase ModelMetrics: Rcpp data.table AmpAffyExample: affy gypsum: utils httr2 jsonlite parallel filelock rappdirs LungCancerACvsSCCGEO: carData: derfinderData: dorothea: dplyr magrittr bcellViper decoupleR htmltools: base64enc digest fastmap grDevices rlang utils sys: evd: stats grDevices graphics fingerprint: methods PWMEnrich.Dmelanogaster.background: methods PWMEnrich glmnet: Matrix methods utils foreach shape survival Rcpp RcppEigen hgu133plus2CellScore: Biobase CellScore: Biobase graphics grDevices gplots lsa methods RColorBrewer squash stats utils SummarizedExperiment CRCL18: Biobase NestLink: AnnotationHub ExperimentHub Biostrings gplots protViz ShortRead grDevices graphics stats utils spatstat.geom: spatstat.data spatstat.univar stats graphics grDevices utils methods spatstat.utils deldir polyclip TFisher: stats sn mvtnorm Matrix purrr: cli lifecycle magrittr rlang vctrs MSMB: tibble BiocSingular: BiocGenerics S4Vectors Matrix methods utils DelayedArray BiocParallel ScaledMatrix irlba rsvd Rcpp beachmat assorthead dcanr: igraph foreach plyr stringr reshape2 methods Matrix graphics stats RColorBrewer circlize doRNG forcats: cli glue lifecycle magrittr rlang tibble ggthemes: ggplot2 graphics grid lifecycle methods purrr scales stringr tibble pRoloc: MSnbase MLInterfaces methods Rcpp BiocParallel stats4 Biobase mclust caret e1071 sampling class kernlab lattice nnet randomForest proxy FNN hexbin BiocGenerics stats dendextend RColorBrewer scales MASS knitr mvtnorm LaplacesDemon coda mixtools gtools plyr ggplot2 biomaRt utils grDevices graphics colorspace RcppArmadillo rprojroot: ecolicdf: utils AnnotationDbi utf8: tidygraph: cli dplyr igraph lifecycle magrittr pillar R6 rlang stats tibble tidyr tools utils cpp11 R2HTML: stats graphics utils grDevices methods bootstrap: stats NCIgraphData: AssessORFData: RSQLite DECIPHER utils breakpointRdata: EGSEAdata: ggExtra: colourpicker ggplot2 grDevices grid gtable miniUI scales shiny shinyjs utils R6 fastcluster: futile.logger: utils lambda.r futile.options hgu95av2.db: methods AnnotationDbi org.Hs.eg.db GenomicInteractions: InteractionSet Rsamtools rtracklayer GenomicRanges IRanges BiocGenerics data.table stringr GenomeInfoDb ggplot2 grid gridExtra methods igraph S4Vectors dplyr Gviz Biobase graphics stats utils grDevices R.methodsS3: utils ecoliLeucine: affy ecolicdf memoise: rlang cachem evaluate: celldex: SummarizedExperiment utils methods Matrix ExperimentHub AnnotationHub AnnotationDbi S4Vectors DelayedArray DelayedMatrixStats gypsum alabaster.base alabaster.matrix alabaster.se DBI RSQLite jsonlite BH: polynom: stats graphics seqLogo: methods grid stats4 grDevices minqa: Rcpp HCATonsilData: ExperimentHub SingleCellExperiment SpatialExperiment HDF5Array SummarizedExperiment S4Vectors htmltools rmarkdown base64enc utils NetActivityData: scATAC.Explorer: SingleCellExperiment BiocFileCache data.table utils S4Vectors zellkonverter methods Matrix Rhdf5lib: GeuvadisTranscriptExpr: units: Rcpp ProtGenerics: methods lumiBarnes: Biobase lumi dotCall64: MsExperiment: ProtGenerics methods S4Vectors IRanges Spectra SummarizedExperiment QFeatures DBI BiocGenerics KEGGREST: methods httr png Biostrings SpatialFeatureExperiment: Biobase BiocGenerics BiocNeighbors BiocParallel data.table DropletUtils EBImage grDevices lifecycle Matrix methods rjson rlang S4Vectors sf sfheaders SingleCellExperiment SpatialExperiment spatialreg spdep SummarizedExperiment stats terra utils zeallot stringdist: parallel ellipse: graphics stats PADOG: KEGGdzPathwaysGEO methods Biobase limma AnnotationDbi GSA foreach doRNG hgu133plus2.db hgu133a.db KEGGREST nlme rstatix: stats utils tidyr purrr broom rlang tibble dplyr magrittr corrplot tidyselect car generics GGally: ggplot2 dplyr tidyr grDevices grid ggstats gtable lifecycle plyr progress RColorBrewer rlang scales utils magrittr lumi: Biobase affy methylumi GenomicFeatures GenomicRanges annotate lattice mgcv nleqslv KernSmooth preprocessCore RSQLite DBI AnnotationDbi MASS graphics stats stats4 methods crosstalk: htmltools jsonlite lazyeval R6 RMassBank: Rcpp assertthat Biobase ChemmineR data.table digest dplyr enviPat glue httr httr2 logger methods MSnbase mzR purrr R.utils rcdk readJDX readr rjson S4Vectors tibble tidyselect webchem XML yaml pan: jomo: stats lme4 survival MASS ordinal tibble MouseGastrulationData: SingleCellExperiment SummarizedExperiment SpatialExperiment methods ExperimentHub BiocGenerics S4Vectors BumpyMatrix RnaSeqSampleSizeData: edgeR gDNAinRNAseqData: RCurl XML ExperimentHub BiocGenerics Rsamtools pryr: codetools lobstr methods Rcpp stringr dbplyr: blob cli DBI dplyr glue lifecycle magrittr methods pillar purrr R6 rlang tibble tidyr tidyselect utils vctrs withr S4Vectors: methods utils stats stats4 BiocGenerics BeadSorted.Saliva.EPIC: minfi ExperimentHub PWMEnrich.Hsapiens.background: methods PWMEnrich OrganismDbi: BiocGenerics AnnotationDbi GenomicFeatures methods utils stats DBI BiocManager Biobase graph RBGL S4Vectors IRanges GenomicRanges txdbmaker SparseM: methods graphics stats utils fontLiberation: ReactomeGSA: Biobase BiocSingular dplyr ggplot2 gplots httr igraph jsonlite methods progress RColorBrewer SummarizedExperiment tidyr HDCytoData: ExperimentHub SummarizedExperiment flowCore utils methods multiWGCNAdata: ExperimentHub utils HumanAffyData: ExperimentHub Biobase affydata: affy methods ggpubr: ggplot2 ggrepel grid ggsci stats utils tidyr purrr dplyr cowplot ggsignif scales gridExtra glue polynom rlang rstatix tibble magrittr furrr: future globals lifecycle purrr rlang vctrs seqinr: ade4 segmented relations: cluster stats slam sets graphics grDevices WES.1KG.WUGSC: aod: methods stats broom.mixed: broom coda dplyr forcats methods nlme purrr stringr tibble tidyr furrr HiBED: dplyr FlowSorted.Blood.EPIC tibble FlowSorted.DLPFC.450k minfi utils AnnotationHub SummarizedExperiment DT: htmltools htmlwidgets httpuv jsonlite magrittr crosstalk jquerylib promises betareg: graphics grDevices methods stats flexmix Formula lmtest modeltools sandwich km.ci: stats survival basilisk: reticulate utils methods parallel dir.expiry basilisk.utils r3dmol: htmlwidgets magrittr methods bio3d LaplacesDemon: parallel grDevices graphics stats utils VariantAnnotation: methods BiocGenerics MatrixGenerics GenomeInfoDb GenomicRanges SummarizedExperiment Rsamtools utils DBI Biobase S4Vectors IRanges XVector Biostrings AnnotationDbi rtracklayer BSgenome GenomicFeatures Rhtslib BiocVersion: BRAIN: PolynomF Biostrings lattice fastmap: TCGAWorkflowData: SummarizedExperiment compositions: methods utils grDevices stats tensorA robustbase bayesm graphics MASS S4Arrays: methods Matrix abind BiocGenerics S4Vectors IRanges stats crayon RnBeads: BiocGenerics S4Vectors GenomicRanges MASS cluster ff fields ggplot2 gplots grid gridExtra limma matrixStats methods illuminaio methylumi plyr IRanges grDevices: stable: rmutil TxDb.Drerio.UCSC.danRer10.refGene: GenomicFeatures AnnotationDbi ape: nlme lattice graphics methods stats utils parallel Rcpp digest TxDb.Dmelanogaster.UCSC.dm6.ensGene: GenomicFeatures AnnotationDbi Cardinal: BiocParallel BiocGenerics ProtGenerics S4Vectors methods stats stats4 CardinalIO Biobase EBImage graphics grDevices irlba Matrix matter nlme parallel utils RANN: crisprScoreData: ExperimentHub AnnotationHub utils SNAGEEdata: QUBICdata: seq2pathway.data: easierData: ExperimentHub AnnotationHub utils SummarizedExperiment phyloseq: ade4 ape Biobase BiocGenerics biomformat Biostrings cluster data.table foreach ggplot2 igraph methods multtest plyr reshape2 scales vegan RTCGA.RPPA: RTCGA knitr: evaluate highr methods tools xfun yaml glmmTMB: methods TMB lme4 Matrix nlme numDeriv mgcv reformulas RcppEigen EnvStats: MASS ggplot2 nortest rbibutils: utils tools GenomicRanges: methods stats4 BiocGenerics S4Vectors IRanges GenomeInfoDb utils stats XVector GUniFrac: Rcpp vegan ggplot2 matrixStats Matrix ape parallel stats utils statmod rmutil dirmult MASS ggrepel foreach modeest inline methods sesame: sesameData graphics BiocParallel utils methods stringr readr tibble MASS wheatmap GenomicRanges IRanges grid preprocessCore S4Vectors ggplot2 BiocFileCache GenomeInfoDb stats SummarizedExperiment dplyr reshape2 hgu133plus2cdf: utils AnnotationDbi HSMMSingleCell: