{ "_id": "6a1ac6fe1d7bb097a09dbd97", "Package": "KEGGgraph", "Type": "Package", "Title": "KEGGgraph: A graph approach to KEGG PATHWAY in R and\nBioconductor", "Version": "1.73.0", "Date": "2025-04-14", "Author": "Jitao David Zhang, with inputs from Paul Shannon and Hervé\nPagès", "Maintainer": "Jitao David Zhang ", "Description": "KEGGGraph is an interface between KEGG pathway and graph\nobject as well as a collection of tools to analyze, dissect and\nvisualize these graphs. It parses the regularly updated KGML\n(KEGG XML) files into graph models maintaining all essential\npathway attributes. The package offers functionalities\nincluding parsing, graph operation, visualization and etc.", "License": "GPL (>= 2)", "LazyLoad": "yes", "LazyData": "yes", "Collate": "kegg2graph-functions.R parse.R annotation.R graph.R kgmlfile.R\nmisc.R vis.R", "URL": "https://accio.github.io/research/#software", "biocViews": "Pathways, GraphAndNetwork, Visualization, KEGG", "Encoding": "UTF-8", "Config/pak/sysreqs": "make libxml2-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:33:37 UTC", "RemoteUrl": "https://github.com/bioc/KEGGgraph", "RemoteRef": "HEAD", "RemoteSha": "ab0d339dd1ac1c93b09f06e5f6a4de949d24e975", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:45:47 UTC", "User": "root" }, "MD5sum": "0ebb53051b9940501172a96d104f73ef", "_user": "bioc", "_type": "src", "_file": "KEGGgraph_1.73.0.tar.gz", "_fileid": "21c208aa088af82e45d8fde93d52ec1ad792cecf049ca85d1ae381fc9db404e9", "_filesize": 1592561, "_sha256": 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"uuid": 1397024 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "XML", "version": ">= 2.3-0", "role": "Imports" }, { "package": "graph", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "RCurl", "role": "Imports" }, { "package": "Rgraphviz", "role": "Imports" }, { "package": "RBGL", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "hgu133plus2.db", "role": "Suggests" }, { "package": "SPIA", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 23, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.73.0", "bioc": "3.24" }, { "branch": "release", "version": "1.72.0", "bioc": "3.23" } ], "_topics": [ "pathways", "graphandnetwork", "visualization", "kegg" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 8887, "source": "https://www.bioconductor.org/packages/stats/bioc/KEGGgraph" }, "_mentions": 39, "_searchresults": 147, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/KEGGgraph.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "edgeData", "edges", "expandKEGGPathway", "getComponent", "getDisplayName", "getEntryID", "getKEGGedgeData", "getKEGGgeneLink", "getKEGGID", "getKEGGnodeData", "getKGMLurl", "getName", "getNamedElement", "getPathwayInfo", "getProduct", "getReactions", "getRgraphvizEdgeNames", "getSubstrate", "getSubtype", "getTitle", "getType", "getValue", "graphDensity", "inEdges", "isHomoList", "KEGGgraphLegend", "KEGGpathway2Graph", "KEGGpathway2reactionGraph", "kgmlFileName2PathwayName", "mergeGraphs", "mergeKEGGgraphs", "neighborhood", "nodeData", "nodes", "nodes<-", "numEdges", "numNodes", "parseEntry", "parseKGML", "parseKGML2DataFrame", "parseKGML2Graph", "parseKGMLexpandMaps", "parsePathwayInfo", "parseReaction", "parseRelation", "plot", "plotKEGGgraph", "pvalue2asterisk", "queryKEGGsubgraph", "randomSubGraph", "retrieveKGML", "show", "splitKEGGgroup", "subGraph", "subGraphByNodeType", "subKEGGgraph", "subtypeDisplay", "translateGeneID2KEGGID", "translateKEGGgraph", "translateKEGGID2GeneID", "ugraph" ], "_datasets": [ { "name": "KEGGEdgeSubtype", "title": "KEGG edge subtypes", "object": "KEGGEdgeSubtype", "class": [ "data.frame" ], "fields": [ "name", "value", "ECrel", "PPrel", "GErel", "Explanation", "color", "label", "fontcolor", "arrowhead", "style" ], "rows": 17, "table": true, "tojson": true }, { "name": "KEGGEdgeType", "title": "KEGG edge types", "object": "KEGGEdgeType", "class": [ "data.frame" ], "fields": [ "value", "explanation" ], "rows": 5, "table": true, "tojson": true }, { "name": "KEGGNodeType", "title": "KEGG node types", "object": "KEGGNodeType", "class": [ "data.frame" ], "fields": [ "value", "explanation" ], "rows": 6, "table": true, "tojson": true }, { "name": "KEGGPATHID2NAME", "title": "KEGG pathway identifier to name", "object": "KEGGPATHID2NAME", "class": [ "AnnDbBimap" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "top", "title": "Colorectal cancer dataset", "topics": [ "top" ] }, { "page": "expandKEGGNode", "title": "Expand KEGG node of paralogues", "topics": [ "expandKEGGNode" ] }, { "page": "expandKEGGPathway", "title": "Expand KEGG Pathway", "topics": [ "expandKEGGPathway" ] }, { "page": "getDisplayName-methods", "title": "Get a character string as label for display", "topics": [ "getDisplayName", "getDisplayName,graph-method", "getDisplayName,KEGGNode-method", "getDisplayName-methods" ] }, { "page": "getEntryID-methods", "title": "Get entry ID for single or list of KEGGNode or KEGGedge object(s)", "topics": [ "getEntryID", "getEntryID,KEGGEdge-method", "getEntryID,KEGGNode-method", "getEntryID,list-method", "getEntryID-methods" ] }, { "page": "getKEGGgeneLink-methods", "title": "Get KEGG gene link", "topics": [ "getKEGGgeneLink", "getKEGGgeneLink,character-method", "getKEGGgeneLink-methods" ] }, { "page": "getKEGGID-methods", "title": "Get KEGG ID", "topics": [ "getKEGGID", "getKEGGID,KEGGNode-method", "getKEGGID-methods" ] }, { "page": "getKEGGnodeData", "title": "Get or set list of KEGG node or edge data", "topics": [ "getKEGGedgeData", "getKEGGnodeData", "setKEGGedgeData", "setKEGGnodeData" ] }, { "page": "getKGMLurl", "title": "Get KGML file (url) with KEGG PATHWAY ID and (optional) organism", "topics": [ "getCategoryIndepKGMLurl", "getKGMLurl", "kgmlNonmetabolicName2MetabolicName", "retrieveKGML" ] }, { "page": "getName-methods", "title": "Get 'name' attribute", "topics": [ "getName", "getName,KEGGEdgeSubtype-method", "getName,KEGGNode-method", "getName,KEGGPathwayInfo-method", "getName-methods" ] }, { "page": "getNamedElement", "title": "Extract the value in a vector by name", "topics": [ "getNamedElement" ] }, { "page": "getPathwayInfo-methods", "title": "Get KEGG pathway info", "topics": [ "getPathwayInfo", "getPathwayInfo,KEGGPathway-method", "getPathwayInfo-methods" ] }, { "page": "getReactions-methods", "title": "Get KEGG reactions", "topics": [ "getReactions", "getReactions,KEGGPathway-method", "getReactions-methods" ] }, { "page": "getRgraphvizEdgeNames", "title": "Get Rgraphviz compatitable edge names", "topics": [ "getRgraphvizEdgeNames" ] }, { "page": "getSubtype-methods", "title": "Get subtype", "topics": [ "getSubtype", "getSubtype,graph-method", "getSubtype,KEGGEdge-method", "getSubtype-methods" ] }, { "page": "getTitle-methods", "title": "Get title for given element", "topics": [ "getTitle", "getTitle-methods" ] }, { "page": "getType-methods", "title": "Get type attribute", "topics": [ "getType", "getType,KEGGEdge-method", "getType,KEGGNode-method", "getType,KEGGReaction-method", "getType-methods" ] }, { "page": "getValue-methods", "title": "Get 'value' attribute", "topics": [ "getValue", "getValue,KEGGEdgeSubtype-method", "getValue-methods" ] }, { "page": "graphDensity", "title": "Graph density", "topics": [ "graphDensity" ] }, { "page": "isHomoList", "title": "Determines whether a list is homogenous", "topics": [ "isHomoList" ] }, { "page": "KEGGEdge-class", "title": "Class 'KEGGEdge'", "topics": [ "entryID<-,KEGGEdge-method", "getName,KEGGEdge-method", "KEGGEdge-class", "show,KEGGEdge-method" ] }, { "page": "KEGGEdgeSubtype", "title": "KEGG edge subtypes", "topics": [ "KEGGEdgeSubtype" ] }, { "page": "KEGGEdgeSubType-class", "title": "Class \"KEGGEdgeSubType\"", "topics": [ "getName,KEGGEdgeSubType-method", "getValue,KEGGEdgeSubType-method", "KEGGEdgeSubType-class", "show,KEGGEdgeSubType-method" ] }, { "page": "KEGGEdgeType", "title": "KEGG edge types", "topics": [ "KEGGEdgeType" ] }, { "page": "KEGGGraphics-class", "title": "class 'KEGGGraphics'", "topics": [ "KEGGGraphics-class" ] }, { "page": "KEGGGroup-class", "title": "Class \"KEGGGroup\"", "topics": [ "getComponent", "getComponent,KEGGGroup-method", "KEGGGroup-class" ] }, { "page": "KEGGNode-class", "title": "Class \"KEGGNode\"", "topics": [ "entryID<-", "entryID<-,KEGGNode-method", "getComponent,KEGGNode-method", "KEGGNode-class", "name<-", "name<-,KEGGNode-method", "show,KEGGNode-method" ] }, { "page": "KEGGNodeType", "title": "KEGG node types", "topics": [ "KEGGNodeType" ] }, { "page": "KEGGPATHID2NAME", "title": "KEGG pathway identifier to name", "topics": [ "KEGGPATHID2NAME" ] }, { "page": "KEGGPathway-class", "title": "Class \"KEGGPathway\"", "topics": [ "edges,KEGGPathway,ANY-method", "edges,KEGGPathway-method", "edges<-", "edges<-,KEGGPathway-method", "getName,KEGGPathway-method", "getTitle,KEGGPathway-method", "KEGGPathway-class", "nodes,KEGGPathway-method", "nodes<-,KEGGPathway,ANY-method", "show,KEGGPathway-method" ] }, { "page": "KEGGpathway2Graph", "title": "Parses KEGGpathway to graph", "topics": [ "KEGGpathway2Graph" ] }, { "page": "KEGGpathway2reactionGraph", "title": "Convert chemical reaction network of KEGG pathway into graph", "topics": [ "KEGGpathway2reactionGraph" ] }, { "page": "KEGGPathwayInfo-class", "title": "Class \"KEGGPathwayInfo\"", "topics": [ "getTitle,KEGGPathwayInfo-method", "KEGGPathwayInfo-class", "show,KEGGPathwayInfo-method" ] }, { "page": "KEGGReaction-class", "title": "Class \"KEGGReaction\"", "topics": [ "getName,KEGGReaction-method", "getProduct", "getProduct,KEGGReaction-method", "getSubstrate", "getSubstrate,KEGGReaction-method", "KEGGReaction-class", "show,KEGGReaction-method" ] }, { "page": "kgmlFileName2PathwayName", "title": "Convert KGML file name to pathway name", "topics": [ "kgmlFileName2PathwayName" ] }, { "page": "mergeGraphs", "title": "A function to merge KEGG graphs", "topics": [ "mergeGraphs" ] }, { "page": "mergeKEGGgraphs", "title": "Merge KEGG graphs, also merging KEGGNode and KEGGEdge attributes", "topics": [ "mergeKEGGgraphs" ] }, { "page": "neighborhood", "title": "Return the neighborhood set of given vertices", "topics": [ "neighborhood" ] }, { "page": "parseEntry", "title": "Parse ENTRY elements of KGML document", "topics": [ "parseEntry" ] }, { "page": "parseGraphics", "title": "Parse 'graphics' elements in KGML files", "topics": [ "parseGraphics" ] }, { "page": "parseKGML", "title": "KGML file parser", "topics": [ "parseKGML" ] }, { "page": "parseKGML2DataFrame", "title": "Parse KGML file into a data frame", "topics": [ "parseKGML2DataFrame" ] }, { "page": "parseKGML2Graph", "title": "Parse KGML files into KEGG graph", "topics": [ "parseKGML2Graph" ] }, { "page": "parseKGMLexpandMaps", "title": "A convenient function to parse KGML and expand its containing maps into one graph object", "topics": [ "parseKGMLexpandMaps" ] }, { "page": "parsePathwayInfo", "title": "Parse information of the pathway from KGML files", "topics": [ "parsePathwayInfo" ] }, { "page": "parseReaction", "title": "Parse reaction from KGML files", "topics": [ "parseReaction" ] }, { "page": "parseRelation", "title": "Parse RELATION elements from KGML files", "topics": [ "parseRelation" ] }, { "page": "parseSubType", "title": "Parse KGML relation subtype", "topics": [ "parseSubType" ] }, { "page": "plotKEGGgraph", "title": "Plot KEGG graph with Rgraphviz", "topics": [ "KEGGgraphLegend", "plotKEGGgraph" ] }, { "page": "pvalue2asterisk", "title": "Return common significance sign (asterisk) associated with given p value", "topics": [ "pvalue2asterisk" ] }, { "page": "queryKEGGsubgraph", "title": "Query the subgraph of a given KEGG graph with Entrez GeneID (s)", "topics": [ "queryKEGGsubgraph" ] }, { "page": "randomSubGraph", "title": "Randomly subset the given graph", "topics": [ "randomSubGraph" ] }, { "page": "splitKEGGgroup", "title": "Split KEGG group", "topics": [ "splitKEGGgroup" ] }, { "page": "subGraphByNodeType", "title": "Subset KEGG graph by node types", "topics": [ "subGraphByNodeType" ] }, { "page": "subKEGGgraph", "title": "Subset KEGG graph, including subsetting node and edge attributes", "topics": [ "subKEGGgraph" ] }, { "page": "subtypeDisplay-methods", "title": "Get display information for relation subtypes", "topics": [ "subtypeDisplay", "subtypeDisplay,graph-method", "subtypeDisplay,KEGGEdge-method", "subtypeDisplay,KEGGEdgeSubType-method", "subtypeDisplay-methods" ] }, { "page": "translateKEGGgraph", "title": "Tranlate the KEGG graph from being indexed by KEGGID to another identifer", "topics": [ "translateKEGGgraph" ] }, { "page": "translateKEGGID2GeneID", "title": "Translate between KEGGID and Entrez Gene ID", "topics": [ "translateGeneID2KEGGID", 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