{ "_id": "6a1af1991d7bb097a09f7438", "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": "2026-05-30 09:43:47 UTC", "User": "root" }, "MD5sum": "15fa2ffc051abf184e22e322cf4f87b0", "_user": "bioc", "_type": "src", "_file": "categoryCompare_1.57.0.tar.gz", "_fileid": "babcd31d36a5d1ca057a867d5948b2238e6c3fd899dc1fe228e2162c7dff74c2", "_filesize": 3297613, "_sha256": "babcd31d36a5d1ca057a867d5948b2238e6c3fd899dc1fe228e2162c7dff74c2", "_created": "2026-05-30T09:43:47.000Z", "_published": "2026-05-30T14:18:01.310Z", "_jobs": [ { "job": 78640465347, "time": 229, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307441409" }, { "job": 78640465387, "time": 381, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307455647" }, { "job": 78640465376, "time": 334, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307450935" }, { "job": 78640465348, "time": 201, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308804345" }, { "job": 78640465349, "time": 204, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308805849" }, { "job": 78639716060, "time": 360, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307271536" }, { "job": 78640465346, "time": 200, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307438790" }, { "job": 78640465382, "time": 287, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307445934" }, { "job": 78640465378, "time": 257, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307443293" }, { "job": 78640465355, "time": 297, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307446772" } ], "_bioccheck": { "error": 2, "warning": 6, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676463066", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/categoryCompare", "_commit": { "id": "05d1e21d8c9b90b23b3308c7d596947d902136c1", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379789 }, "_maintainer": { "name": "Robert M. 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false, "tojson": true }, { "name": "table10", "title": "Test data for 'categoryCompare'", "object": "ccData", "file": "ccData.RData", "class": [ "data.frame" ], "fields": [ "ID", "logFC", "AveExpr", "t", "P.Value", "adj.P.Val", "B", "Entrez" ], "rows": 100, "table": true, "tojson": true }, { "name": "table48", "title": "Test data for 'categoryCompare'", "object": "ccData", "file": "ccData.RData", "class": [ "data.frame" ], "fields": [ "ID", "logFC", "AveExpr", "t", "P.Value", "adj.P.Val", "B", "Entrez" ], "rows": 100, "table": true, "tojson": true } ], "_help": [ { "page": "categoryCompare-package", "title": "Meta-analysis of high-throughput experiments using feature annotations", "topics": [ "categoryCompare-package", "categoryCompare" ] }, { "page": "breakEdges-methods", "title": "Methods for Function 'breakEdges' in Package 'categoryCompare'", "topics": [ "breakEdges", "breakEdges,ccCompareResult,numeric-method", "breakEdges,numeric,numeric-method", "breakEdges-methods" ] }, { "page": "ccCompare", "title": "Comparison of enriched annotations", "topics": [ "ccCompare", "ccCompare,ccEnrichCollection,ccOptions-method", "ccCompare,GENccEnrichResult,ccOptions-method", "ccCompare,GOccEnrichResult,ccOptions-method", "ccCompare,KEGGccEnrichResult,ccOptions-method", "ccCompare-methods" ] }, { "page": "ccCompareCollection-class", "title": "Class '\"ccCompareCollection\"'", "topics": [ "ccCompareCollection", "ccCompareCollection-class" ] }, { "page": "ccCompareGeneric-methods", "title": "Methods for Function 'ccCompareGeneric' in Package 'categoryCompare'", "topics": [ "ccCompareGeneric", "ccCompareGeneric-methods", "ccOptions,ccCompareGeneric-method", "GENccEnrichResult,ccCompareGeneric-method" ] }, { "page": "ccCompareResult-class", "title": "Class '\"ccCompareResult\"'", "topics": [ "allAnnotation", "allAnnotation,ccCompareResult-method", "ccCompareResult", "ccCompareResult-class", "mainGraph", "mainGraph,ccCompareResult-method", "mainTable", "mainTable,ccCompareResult-method" ] }, { "page": "ccData", "title": "Test data for 'categoryCompare'", "topics": [ "ccData", "ccOpts", "ccResults", "ccResultsBPHier", "enrichLists", "geneLists", "gseaRes", "gUniverse", "table10", "table48" ] }, { "page": "ccEnrich", "title": "Perform annotation enrichment for multiple gene lists", "topics": [ "ccEnrich", "ccEnrich,ccGeneList-method", "ccEnrich-method" ] }, { "page": "ccEnrichCollection-class", "title": "Class \"ccEnrichCollection\"", "topics": [ "ccEnrichCollection", "ccEnrichCollection-class", "graphType,ccEnrichCollection-method", "graphType<-,ccEnrichCollection-method", "minCount<-,ccEnrichCollection-method", "pvalueCutoff<-,ccEnrichCollection-method", "pvalueType<-,ccEnrichCollection-method" ] }, { "page": "ccEnrichResult-class", "title": "Class \"ccEnrichResult\"", "topics": [ "ccEnrichResult", "ccEnrichResult-class", "fdr,ccEnrichResult-method", "GOccEnrichResult", "GOccEnrichResult-class", "graphType,ccEnrichResult-method", "graphType<-,ccEnrichResult-method", "KEGGccEnrichResult", "KEGGccEnrichResult-class", "minCount,ccEnrichResult-method", "minCount<-,ccEnrichResult-method", "pvalueCutoff,ccEnrichResult-method", "pvalueCutoff<-,ccEnrichResult-method", "pvalueType,ccEnrichResult-method", "pvalueType<-,ccEnrichResult-method", "[,ccEnrichResult,ANY,ANY,ANY-method", "[,ccEnrichResult,ANY,ANY-method" ] }, { "page": "ccGeneList-class", "title": "Class \"ccGeneList\"", "topics": [ "ccGeneList", "ccGeneList-class", "ccType", "ccType,ccGeneList-method", "ccType<-", "ccType<-,ccGeneList-method", "fdr,ccGeneList-method", "fdr<-,ccGeneList-method", "listNames,ccGeneList-method", "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", "HyperGParamsCC", "HyperGParamsCC-class", "KEGGHyperGParams", "KEGGHyperGParams-class", "KEGGHyperGParamsCC", "KEGGHyperGParamsCC-class" ] }, { "page": "HyperGResultCC-class", "title": "Class \"HyperGResultCC\"", "topics": [ "fdr,HyperGResultCC-method", "fdrvalues", "fdrvalues,HyperGResultCC-method", "fdrvalues-method", "GOHyperGResultCC", 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