{ "_id": "6ae75b3c2e87f76f20acd058", "Package": "categoryCompare", "Version": "1.57.0", "Title": "Meta-analysis of high-throughput experiments using feature\nannotations", "Author": "Robert M. Flight ", "Maintainer": "Robert M. Flight ", "URL": "https://github.com/rmflight/categoryCompare", "BugReports": "https://github.com/rmflight/categoryCompare/issues", "License": "GPL-2", "LazyLoad": "yes", "Description": "Calculates significant annotations (categories) in each of\ntwo (or more) feature (i.e. gene) lists, determines the overlap\nbetween the annotations, and returns graphical and tabular data\nabout the significant annotations and which combinations of\nfeature lists the annotations were found to be significant.\nInteractive exploration is facilitated through the use of\nRCytoscape (heavily suggested).", "SystemRequirements": "Cytoscape (>= 3.6.1) (if used for visualization of\nresults, heavily suggested)", "TODO": "Text and HTML output without graphs.", "biocViews": "Annotation, GO, MultipleComparison, Pathways, GeneExpression", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev python3 libzmq3-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:36:29 UTC", "RemoteUrl": "https://github.com/bioc/categoryCompare", "RemoteRef": "HEAD", "RemoteSha": "05d1e21d8c9b90b23b3308c7d596947d902136c1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-01 13:26:21 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "categoryCompare_1.57.0.tar.gz", "_fileid": "https://r2.ropensci.org/65257f9ff27b37ffb2fe0f364416940ac050dca4df5a9b0c637feeb62c3192fb", "_filesize": 3300264, "_sha256": "65257f9ff27b37ffb2fe0f364416940ac050dca4df5a9b0c637feeb62c3192fb", "_expires": "2027-02-09T15:31:06.000Z", "_created": "2026-11-01T13:26:21.000Z", "_published": "2026-11-01T15:31:08.322Z", "_upstream": "https://github.com/bioc/categoryCompare", "_status": "success", "_maintainer": { "name": "Robert M. 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"pvalueCutoff,ccGeneList-method", "pvalueCutoff<-,ccGeneList-method", "testDirection,ccGeneList-method" ] }, { "page": "ccOptions-class", "title": "Class \"ccOptions\"", "topics": [ "ccOptions", "ccOptions-class", "compareColors", "compareColors,ccOptions-method", "compareColors<-", "compareColors<-,ccOptions-method", "compareIndx", "compareIndx,ccOptions-method", "compareNames", "compareNames,ccOptions-method", "compareNames<-", "compareNames<-,ccOptions-method", "cssClass", "cssClass,ccOptions-method", "listNames,ccOptions-method", "listNames<-,ccOptions-method", "outType", "outType,ccOptions-method", "outType<-", "outType<-,ccOptions-method" ] }, { "page": "ccOutCyt-methods", "title": "Methods for Function 'ccOutCyt' in Package 'categoryCompare'", "topics": [ "ccOutCyt", "ccOutCyt,ccCompareResult,ccOptions-method", "ccOutCyt-methods" ] }, { "page": "ccSigList-class", "title": "Class '\"ccSigList\"'", "topics": [ "annotation,ccSigList-method", "category,ccSigList-method", "ccSigList", "ccSigList-class", "ontology,ccSigList-method", "sigID,ccSigList-method" ] }, { "page": "cwReload-methods", "title": "Methods for Function 'cwReload' in Package 'categoryCompare'", "topics": [ "cwReload", "cwReload,numeric,ccOptions-method", "cwReload,numeric,character,ccOptions-method", "cwReload-methods" ] }, { "page": "cytOutData-methods", "title": "Methods for Function 'cytOutData'", "topics": [ "cytOutData", "cytOutData,list,ccCompareResult,mergedData-method", "cytOutData,list,ccCompareResult,missing-method", "cytOutData,list,missing,missing-method", "cytOutData-methods" ] }, { "page": "cytOutNodes-methods", "title": "Methods for Function 'cytOutNodes'", "topics": [ "cytOutNodes", "cytOutNodes,character,numeric,list-method", "cytOutNodes,character,numeric,missing-method", "cytOutNodes-methods" ] }, { "page": "fdr", "title": "Number of FDR runs to perform", "topics": [ "fdr", "fdr<-" ] }, { "page": "GENccEnrichResult-class", "title": "Class '\"GENccEnrichResult\"'", "topics": [ "category,GENccEnrichResult-method", "ccCompareGeneric,GENccEnrichResult,ccOptions-method", "GENccEnrichResult", "GENccEnrichResult-class", "geneAnnMapping", "geneAnnMapping,GENccEnrichResult-method", "graphType,GENccEnrichResult-method", "graphType<-,GENccEnrichResult-method", "ontology,GENccEnrichResult-method", "sigID", "[,GENccEnrichResult,ANY,ANY,ANY-method", "[,GENccEnrichResult,ANY,ANY-method" ] }, { "page": "getGeneSymbol", "title": "Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion.", "topics": [ "getAnnotation", "getGeneName", "getGeneSymbol", "getGO2ALLEGS", "getPATH2EG" ] }, { "page": "graphType-methods", "title": "graphType", "topics": [ "graphType", "graphType-methods", "graphType<-" ] }, { "page": "HyperGParamsCC-class", "title": "Class \"HyperGParamsCC\"", "topics": [ "fdr,HyperGParamsCC-method", "fdr<-,HyperGParamsCC-method", "GOHyperGParams", "GOHyperGParams-class", "GOHyperGParamsCC", "GOHyperGParamsCC-class", 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