{ "_id": "6a1acbdc1d7bb097a09de312", "Package": "graph", "Title": "graph: A package to handle graph data structures", "Version": "1.91.0", "Authors@R": "c(\nperson(\"R\", \"Gentleman\", role = \"aut\"),\nperson(\"Elizabeth\", \"Whalen\", role=\"aut\"),\nperson(\"W\", \"Huber\", role=\"aut\"),\nperson(\"S\", \"Falcon\", role=\"aut\"),\nperson(\"Jeff\", \"Gentry\", role=\"aut\"),\nperson(\"Paul\", \"Shannon\", role=\"aut\"),\nperson(\"Halimat C.\", \"Atanda\", role = \"ctb\",\ncomment = \"Converted 'MultiGraphClass' and 'GraphClass' vignettes from Sweave to RMarkdown / HTML.\"\n),\nperson(\"Paul\", \"Villafuerte\", role = \"ctb\",\ncomment = \"Converted vignettes from Sweave to RMarkdown / HTML.\"\n),\nperson(\"Aliyu Atiku\", \"Mustapha\", role = \"ctb\",\ncomment = \"Converted 'Graph' vignette from Sweave to RMarkdown / HTML.\"\n),\nperson(\"Bioconductor Package Maintainer\", role = \"cre\",\nemail = \"maintainer@bioconductor.org\"\n))", "Description": "A package that implements some simple graph handling\ncapabilities.", "License": "Artistic-2.0", "Collate": "AllClasses.R AllGenerics.R bitarray.R buildDepGraph.R\nmethods-graph.R graphNEL.R clustergraph.R NELhandler.R\nedgefunctions.R graphfunctions.R GXLformals.R gxlReader.R\nrandom.R write.tlp.R mat2graph.R settings.R zzz.R\nstandardLabeling.R TODOT.R toDotWithRI.R methods-graphAM.R\nattrData.R reverseEdgeDirections.R nodes-methods.R\nmethods-multiGraph.R MultiGraph.R methods-graphBAM.R\ngraph-constructors.R", "LazyLoad": "yes", "Packaged": { "Date": "2026-05-30 08:04:42 UTC", "User": "root" }, "biocViews": "GraphAndNetwork", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:30:05 UTC", "RemoteUrl": "https://github.com/bioc/graph", "RemoteRef": "HEAD", "RemoteSha": "ffac7de9cbac3adc7cd254d6a6c1c00359356b8f", "NeedsCompilation": "yes", "Author": "R Gentleman [aut],\nElizabeth Whalen [aut],\nW Huber [aut],\nS Falcon [aut],\nJeff Gentry [aut],\nPaul Shannon [aut],\nHalimat C. Atanda [ctb] (Converted 'MultiGraphClass' and 'GraphClass'\nvignettes from Sweave to RMarkdown / HTML.),\nPaul Villafuerte [ctb] (Converted vignettes from Sweave to RMarkdown /\nHTML.),\nAliyu Atiku Mustapha [ctb] (Converted 'Graph' vignette from Sweave to\nRMarkdown / HTML.),\nBioconductor Package Maintainer [cre]", "Maintainer": "Bioconductor Package Maintainer ", "MD5sum": "465034db38c4def6b9d6982a10e49b63", "_user": "bioc", "_type": "src", "_file": "graph_1.91.0.tar.gz", "_fileid": "6e0d2d73bf7405db634ae0310b74ccd90d90ef0a91b04d2057755188a7fb165f", "_filesize": 719082, "_sha256": "6e0d2d73bf7405db634ae0310b74ccd90d90ef0a91b04d2057755188a7fb165f", "_created": "2026-05-30T08:04:42.000Z", "_published": "2026-05-30T11:37:00.740Z", "_jobs": [ { "job": 78635401353, "time": 168, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306708103" }, { "job": 78635401407, "time": 182, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7306709487" }, { "job": 78635401390, "time": 213, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7306712504" }, { "job": 78635401388, "time": 191, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7306710297" }, { "job": 78635401385, "time": 176, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7306708816" }, { "job": 78635401399, "time": 132, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7307892199" }, { "job": 78635401394, "time": 221, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7306713773" }, { "job": 78635401393, "time": 105, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7307891068" }, { "job": 78635401392, "time": 272, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7306718758" }, { "job": 78635233606, "time": 191, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306691429" }, { "job": 78635401368, "time": 113, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306702698" }, { "job": 78635401372, "time": 123, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7306703689" }, { "job": 78635401361, "time": 132, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7306704601" }, { "job": 78635401364, "time": 129, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7306704263" } ], "_bioccheck": { "error": 1, "warning": 4, "note": 19 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678725383", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/graph", "_commit": { "id": "ffac7de9cbac3adc7cd254d6a6c1c00359356b8f", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379405 }, "_maintainer": { "name": "Bioconductor Package Maintainer", "email": "maintainer@bioconductor.org", "login": "bioconductor-bot", "description": "", "uuid": 11681645 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "BiocGenerics", "version": ">= 0.13.11", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "stats4", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "SparseM", "version": ">= 0.36", "role": "Suggests" }, { "package": "XML", "role": "Suggests" }, { "package": "RBGL", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "cluster", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "Rgraphviz", "role": "Enhances" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 342, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2025-49", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.91.0", "bioc": "3.24" }, { "branch": "release", "version": "1.90.0", "bioc": "3.23" } ], "_topics": [ "graphandnetwork" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 34478, "source": "https://www.bioconductor.org/packages/stats/bioc/graph" }, "_mentions": 45, "_searchresults": 924, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/graph.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_releases": [ { "version": "1.14.2", "date": "2007-06-01" }, { "version": "1.15.6", "date": "2007-10-03" }, { "version": "1.16.1", "date": "2008-01-24" }, { "version": "1.17.15", "date": "2008-04-22" }, { "version": "1.18.0", "date": "2008-05-05" }, { "version": "1.19.6", "date": "2008-10-08" }, { "version": "1.20.0", "date": "2008-11-28" }, { "version": "1.22.2", "date": "2009-05-10" }, { "version": "1.24.1", "date": "2009-11-13" }, { "version": "1.26.0", "date": "2010-04-28" }, { "version": "1.28.0", "date": "2010-10-26" }, { "version": "1.30.0", "date": "2011-04-26" } ], "_exports": [ ".dropEdges", ".ftM2other", "acc", "addEdge", "addNode", "adj", "adjacencyMatrix", "aM2bpG", "attrDataItem", "attrDataItem<-", "attrDefaults", "attrDefaults<-", "aveNumEdges", "boundary", "buildRepDepGraph", "calcProb", "calcSumProb", "clearNode", "clusteringCoefficient", "coerce", "combineNodes", "complement", "connComp", "degree", "DFS", "Dist", "dumpGXL", "duplicatedEdges", "edgeData", "edgeData<-", "edgeDataDefaults", "edgeDataDefaults<-", "edgeL", "edgeMatrix", "edgemode", "edgemode<-", "edgeNames", "edgeRenderInfo", "edgeRenderInfo<-", "edges", "edgeSetIntersect0", "edgeSets", "edgeSetUnion0", "edgeWeights", "eweights", "eWV", "extractFromTo", "extractGraphAM", "extractGraphBAM", "fromGXL", "ftM2adjM", "ftM2graphNEL", "ftM2int", "graph.par", "graph.par.get", "graph2SparseM", "graphAM", "graphBAM", "graphIntersect", "graphNEL", "graphRenderInfo", "graphRenderInfo<-", "graphUnion", "gxlTreeNEL", "inEdges", "initialize", "int2ftM", "intersection", "intersection2", "isAdjacent", "isConnected", "isDirected", "join", "leaves", "listEdges", "mgEdgeData", "mgEdgeData<-", "mgEdgeDataDefaults", "mgEdgeDataDefaults<-", "mostEdges", "MultiGraph", "nodeData", "nodeData<-", "nodeDataDefaults", "nodeDataDefaults<-", "nodeRenderInfo", "nodeRenderInfo<-", "nodes", "nodes<-", "numEdges", "numNodes", "numNoEdges", "parRenderInfo", "parRenderInfo<-", "pathWeights", "plot", "randomEGraph", "randomGraph", "randomNodeGraph", "removeAttrDataItem<-", "removeEdge", "removeEdgesByWeight", "removeNode", "reverseEdgeDirections", "show", "sparseM2Graph", "subGraph", "subsetEdgeSets", "threshold", "toDotR", "toDotWithRI", "toGXL", "ugraph", "ugraphOld", "union", "updateGraph", "validateGXL", "validGraph" ], "_datasets": [ { "name": "apopGraph", "title": "KEGG apoptosis pathway graph", "object": "apopGraph", "file": "apopGraph.rda", "class": [ "graphNEL" ], "fields": [], "table": false, "tojson": false }, { "name": "biocRepos", "title": "A graph representing the Bioconductor package repository", "object": "biocRepos", "file": "biocRepos.rda", "class": [ "graphNEL" ], "fields": [], "table": false, "tojson": false }, { "name": "esetsFemale", "title": "MultiGraph edgeSet data", "object": "esetsFemale", "file": "esetsFemale.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "esetsMale", "title": "MultiGraph edgeSet data", "object": "esetsMale", "file": "esetsMale.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "graphExamples", "title": "A List Of Example Graphs", "object": "graphExamples", "file": "graphExamples.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "IMCAAttrs", "title": "KEGG Integrin Mediated Cell Adhesion graph", "object": "integrinMediatedCellAdhesion", "file": "integrinMediatedCellAdhesion.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "IMCAGraph", "title": "KEGG Integrin Mediated Cell Adhesion graph", "object": "integrinMediatedCellAdhesion", "file": "integrinMediatedCellAdhesion.rda", "class": [ "graphNEL" ], "fields": [], "table": false, "tojson": false }, { "name": "MAPKsig", "title": "A graph encoding parts of the MAPK signaling pathway", "object": "defunctGraph", "file": "defunctGraph.rda", "class": [ "graphNEL" ], "fields": [], "table": false, "tojson": false }, { "name": "MAPKsig", "title": "A graph encoding parts of the MAPK signaling pathway", "object": "MAPKsig", "file": "MAPKsig.rda", "class": [ "graphNEL" ], "fields": [], "table": false, "tojson": false }, { "name": "pancrCaIni", "title": "A graph encoding parts of the pancreatic cancer initiation pathway", "object": "pancrCaIni", "file": "pancrCaIni.rda", "class": [ "graphNEL" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "acc-methods", "title": "Methods for Accessibility Lists", "topics": [ "acc", "acc,clusterGraph,character-method", "acc,clusterGraph-method", "acc,graph,character-method", "acc,graph-method", "acc-methods" ] }, { "page": "addEdge", "title": "addEdge", "topics": [ "addEdge" ] }, { "page": "addNode", "title": "addNode", "topics": [ "addNode", "addNode,character,distGraph,list-method", "addNode,character,graphBAM,missing-method", "addNode,character,graphNEL,list-method", "addNode,character,graphNEL,missing-method" ] }, { "page": "adj-methods", "title": "Methods for finding the adjacency list for selected nodes.", "topics": [ "adj", "adj-methods" ] }, { "page": "adjacencyMatrix", "title": "Compute an Adjacency Matrix for a graphBAM object", "topics": [ "adjacencyMatrix", "adjacencyMatrix,graphBAM-method" ] }, { "page": "apoptosisGraph", "title": "KEGG apoptosis pathway graph", "topics": [ "apopAttrs", "apopGraph", "apopLocusLink" ] }, { "page": "attrData-class", "title": "Class \"attrData\"", "topics": [ "attrData-class", "attrDataItem,attrData,character,character-method", "attrDataItem,attrData,character,missing-method", "attrDataItem<-,attrData,character,character-method", "attrDefaults,attrData,character-method", "attrDefaults,attrData,missing-method", "attrDefaults<-,attrData,character,ANY-method", "attrDefaults<-,attrData,missing,list-method", "initialize,attrData-method", "names,attrData-method", "names<-,attrData,character-method", "removeAttrDataItem<-", "removeAttrDataItem<-,attrData,character,NULL-method" ] }, { "page": "attrDataItem-methods", "title": "Get and set attributes values for items in an attrData object", "topics": [ "attrDataItem", "attrDataItem-methods", "attrDataItem<-", "attrDataItem<--methods" ] }, { "page": "attrDefaults-methods", "title": "Get and set the default attributes of an attrData object", "topics": [ "attrDefaults", "attrDefaults-methods", "attrDefaults<-", "attrDefaults<--methods" ] }, { "page": "aveNumEdges", "title": "Calculate the average number of edges in a graph", "topics": [ "aveNumEdges" ] }, { "page": "biocRepos", "title": "A graph representing the Bioconductor package repository", "topics": [ "biocRepos" ] }, { "page": "boundary", "title": "Returns the Boundary between a Graph and a SubGraph", "topics": [ "boundary" ] }, { "page": "calcProb", "title": "Calculate the hypergeometric probability of the subgraph's number of edges.", "topics": [ "calcProb" ] }, { "page": "calcSumProb", "title": "Calculate the probability that a subgraph has an unusual number of edges.", "topics": [ "calcSumProb" ] }, { "page": "clearNode", "title": "clearNode", "topics": [ "clearNode" ] }, { "page": "clusterGraph-class", "title": "Class \"clusterGraph\"", "topics": [ "adj,clusterGraph,ANY-method", "clusterGraph-class", "coerce,clusterGraph,matrix-method", "connComp,clusterGraph-method", "edgeL,clusterGraph-method", "edges,clusterGraph-method", "edgeWeights,clusterGraph,ANY-method", "edgeWeights,clusterGraph-method", "nodes,clusterGraph-method", "nodes<-,clusterGraph,character-method", "numNodes,clusterGraph-method", "show,clusterGraph-method" ] }, { "page": "clusteringCoefficient-methods", "title": "Clustering coefficient of a graph", "topics": [ "clusteringCoefficient", "clusteringCoefficient,graph", "clusteringCoefficient,graph-method" ] }, { "page": "matrix2Graph", "title": "Coercions between matrix and graph representations", "topics": [ "aM2bpG", "coerce,graphNEL,matrix-method", "coerce,matrix,graphNEL-method", "ftM2adjM", "ftM2graphNEL" ] }, { "page": "combineNodes", "title": "combineNodes", "topics": [ "combineNodes", "combineNodes,character,graphNEL,character-method" ] }, { "page": "DFS", "title": "Depth First Search", "topics": [ "DFS", "DFS,graph,character-method" ] }, { "page": "distGraph-class", "title": "Class \"distGraph\"", "topics": [ "adj,distGraph,ANY-method", "Dist", "Dist,distGraph-method", "distGraph-class", "edgeL,distGraph-method", "edges,distGraph-method", "edgeWeights,distGraph,ANY-method", "edgeWeights,distGraph-method", "initialize,distGraph-method", "nodes,distGraph-method", "numNodes,distGraph-method", "show,distGraph-method", "threshold", "threshold,distGraph-method", "[.dist" ] }, { "page": "duplicatedEdges", "title": "duplicatedEdges", "topics": [ "duplicatedEdges" ] }, { "page": "edgeData-methods", "title": "Get and set attributes for the edges of a graph object", "topics": [ "edgeData", "edgeData-methods", "edgeData<-", "edgeData<--methods" ] }, { "page": "edgeDataDefaults-methods", "title": "Get and set default attributes for the edges of a graph", "topics": [ "edgeDataDefaults", "edgeDataDefaults-methods", "edgeDataDefaults<-", "edgeDataDefaults<--methods" ] }, { "page": "edgeMatrix", "title": "Compute an Edge Matrix or weight vector for a Graph", "topics": [ "edgeMatrix", "edgeMatrix,clusterGraph-method", "edgeMatrix,distGraph-method", "edgeMatrix,graphAM-method", "edgeMatrix,graphBAM-method", "edgeMatrix,graphNEL-method", "eWV", "pathWeights" ] }, { "page": "edgeSets", "title": "MultiGraph edgeSet data", "topics": [ "esetsFemale", "esetsMale" ] }, { "page": "edgeWeights", "title": "Retrieve the edge weights of a graph", "topics": [ "edgeWeights" ] }, { "page": "fromGXL-methods", "title": "Methods for GXL manipulations in package graph", "topics": [ "dumpGXL", "dumpGXL,connection-method", "dumpGXL-methods", "fromGXL", "fromGXL,connection-method", "fromGXL-methods", "GXL", "gxlTreeNEL", "NELhandler", "toGXL", "toGXL-methods", "validateGXL", "validateGXL,connection-method" ] }, { "page": "graph-class", "title": "Class \"graph\"", "topics": [ "complement", "complement,graph-method", "connComp", "connComp,graph-method", "degree", "degree,graph-method", "degree,MultiGraph-method", "dfs,graph-method", "edgeData,graph,character,character,character-method", "edgeData,graph,character,character,missing-method", "edgeData,graph,character,missing,character-method", "edgeData,graph,missing,character,character-method", "edgeData,graph,missing,missing,character-method", "edgeData,graph,missing,missing,missing-method", "edgeData<-,graph,character,character,character,ANY-method", "edgeData<-,graph,character,character,character-method", "edgeData<-,graph,character,missing,character,ANY-method", "edgeData<-,graph,character,missing,character-method", "edgeData<-,graph,missing,character,character,ANY-method", "edgeData<-,graph,missing,character,character-method", "edgeDataDefaults,graph,character-method", "edgeDataDefaults,graph,missing-method", "edgeDataDefaults<-,graph,character,ANY-method", "edgeDataDefaults<-,graph,character-method", "edgeDataDefaults<-,graph,missing,list-method", "edgeL,graph-method", "edgemode", "edgemode,graph-method", "edgemode<-", "edgemode<-,graph,character-method", "edgeNames", "edgeNames,graph-method", "edgeWeights,graph,character-method", "edgeWeights,graph,missing-method", "edgeWeights,graph,numeric-method", "graph-class", "graphBase-class", "intersection", "intersection,graph,graph-method", "intersection2", "intersection2,graph,graph-method", "isAdjacent,graph,character,character-method", "isConnected", "isConnected,graph-method", "isDirected,graph-method", "join", "join,graph,graph-method", "nodeData,graph,character,character-method", "nodeData,graph,character,missing-method", "nodeData,graph,missing,character-method", "nodeData,graph,missing,missing-method", "nodeData<-,graph,character,character-method", "nodeData<-,graph,missing,character-method", "nodeDataDefaults,graph,character-method", "nodeDataDefaults,graph,missing-method", "nodeDataDefaults<-,graph,character,ANY-method", "nodeDataDefaults<-,graph,character-method", "nodeDataDefaults<-,graph,missing,list-method", "nodes,graph-method", "nodes<-,graph,character-method", "numEdges", "numEdges,graph-method", "numNodes", "numNodes,graph-method", "plot,graph,ANY-method", "plot,graph-method", "show,graph-method", "union,graph,graph-method", "updateGraph", "updateGraph,graph-method" ] }, { "page": "defunct", "title": "Defunct Functions in Package 'graph'", "topics": [ "buildRepDepGraph", "graph-defunct", "pkgInstOrder", "ugraphOld" ] }, { "page": "settings", "title": "Graphical parameters and other settings", "topics": [ "graph.par", "graph.par.get" ] }, { "page": "graph2SparseM", "title": "Coercion methods between graphs and sparse matrices", "topics": [ "graph2SparseM", "sparseM2Graph" ] }, { "page": "graphAM-class", "title": "Class \"graphAM\"", "topics": [ "addEdge,character,character,graphAM,missing-method", "addNode,character,graphAM,missing-method", "clearNode,character,graphAM-method", "coerce,graphAM,graphBAM-method", "coerce,graphAM,graphNEL-method", "coerce,graphAM,matrix-method", "coerce,matrix,graphAM-method", "edges,graphAM-method", "graphAM", "graphAM-class", "inEdges,character,graphAM-method", "inEdges,graphAM,missing-method", "inEdges,missing,graphAM-method", "initialize,graphAM-method", "isAdjacent,graphAM,character,character-method", "nodes,graphAM-method", "nodes<-,graphAM,character-method", "numEdges,graphAM-method", "numNodes,graphAM-method", "removeEdge,character,character,graphAM-method", "removeNode,character,graphAM-method" ] }, { "page": "graphBAM-class", "title": "EXPERIMENTAL class \"graphBAM\"", "topics": [ "addEdge,character,character,graphBAM,missing-method", "addEdge,character,character,graphBAM,numeric-method", "adj,graphBAM,character-method", "clearNode,character,graphBAM-method", "coerce,graphBAM,graphAM-method", "coerce,graphBAM,graphNEL-method", "coerce,graphBAM,matrix-method", "edgeData,graphBAM,character,character,character-method", "edgeData,graphBAM,character,missing,character-method", "edgeData,graphBAM,missing,character,character-method", "edgeData,graphBAM,missing,missing,character-method", "edgeData,graphBAM,missing,missing,missing-method", "edgeData<-,graphBAM,character,character,character,ANY-method", "edgeData<-,graphBAM,character,character,character-method", "edgeData<-,graphBAM,character,missing,character,ANY-method", "edgeData<-,graphBAM,character,missing,character-method", "edgeData<-,graphBAM,missing,character,character,ANY-method", "edgeData<-,graphBAM,missing,character,character-method", "edgeData<-,graphBAM,missing,missing,character,ANY-method", "edgeData<-,graphBAM,missing,missing,character-method", "edgeDataDefaults<-,graphBAM,character,ANY-method", "edgeDataDefaults<-,graphBAM,missing,list-method", "edgemode<-,graphBAM,character-method", "edges,graphBAM-method", "edgeWeights,graphBAM,character-method", "edgeWeights,graphBAM,missing-method", "edgeWeights,graphBAM,numeric-method", "edgeWeights,graphBAM-method", "extractFromTo,graphBAM-method", "graphBAM", "graphBAM-class", "graphIntersect", "graphIntersect,graphBAM,graphBAM-method", "graphUnion", "graphUnion,graphBAM,graphBAM-method", "inEdges,character,graphBAM-method", "initialize,graphBAM-method", "isAdjacent,graphBAM,character,character-method", "nodeData,graphBAM,character,character-method", "nodeData,graphBAM,character,missing-method", "nodeData,graphBAM,missing,character-method", "nodeData,graphBAM,missing,missing-method", "nodeData<-,graphBAM,character,character-method", "nodeData<-,graphBAM,missing,character-method", "nodeDataDefaults,graphBAM,character-method", "nodeDataDefaults,graphBAM,missing-method", "nodeDataDefaults<-,graphBAM,character,ANY-method", "nodeDataDefaults<-,graphBAM,missing,ANY-method", "nodeDataDefaults<-,graphBAM,missing,list-method", "nodes,graphBAM-method", "nodes<-,graphBAM,character-method", "numEdges,graphBAM-method", "numNodes,graphBAM-method", "removeEdge,character,character,graphBAM-method", "removeEdgesByWeight", "removeEdgesByWeight,graphBAM-method", "removeNode,character,graphBAM-method", "show,graphBAM-method", "ugraph,graphBAM-method" ] }, { "page": "graphExamples", "title": "A List Of Example Graphs", "topics": [ "graphExamples" ] }, { "page": "graphNEL-class", "title": "Class \"graphNEL\"", "topics": [ "addEdge,character,character,graphNEL,missing-method", "addEdge,character,character,graphNEL,numeric-method", "addNode,character,graphNEL-method", "adj,graphNEL,ANY-method", "clearNode,character,graphNEL-method", "coerce", "coerce,graphNEL,generalGraph-method", "coerce,graphNEL,graphAM-method", "coerce,graphNEL,graphBAM-method", "edgeL", "edgeL,graphNEL-method", "edges", "edges,graphNEL-method", "edgeWeights,graphNEL-method", "graphNEL", "graphNEL-class", "inEdges,character,graphNEL-method", "inEdges,graphNEL,missing-method", "inEdges,missing,graphNEL-method", "initialize", "initialize,graphNEL-method", "nodes", "nodes,graphNEL-method", "nodes<-", "nodes<-,graphNEL,character-method", "numNodes,graphNEL-method", "removeEdge,character,character,graphNEL-method", "removeNode,character,graphNEL-method", "toGXL,graphNEL-method" ] }, { "page": "inEdges", "title": "Generic Method inEdges", "topics": [ "inEdges" ] }, { "page": "IMCA", "title": "KEGG Integrin Mediated Cell Adhesion graph", "topics": [ "IMCA", "IMCAAttrs", "IMCAGraph", "integrinMediatedCellAdhesion" ] }, { "page": "isAdjacent-methods", "title": "Determine if nodes share an edge in a graph", "topics": [ "isAdjacent", "isAdjacent-methods" ] }, { "page": "isDirected-methods", "title": "Determine if a graph has directed or undirected edges", "topics": [ "isDirected", "isDirected-methods" ] }, { "page": "leaves", "title": "Find the leaves of a graph", "topics": [ "leaves", "leaves,graph-method" ] }, { "page": "listEdges", "title": "List the Edges of a Graph", "topics": [ "listEdges" ] }, { "page": "MAPKsig", "title": "A graph encoding parts of the MAPK signaling pathway", "topics": [ "MAPKsig" ] }, { "page": "mostEdges", "title": "Find the node in a graph with the greatest number of edges", "topics": [ "mostEdges" ] }, { "page": "multigraph", "title": "Class \"multiGraph\"", "topics": [ "edgemode,edgeSet-method", "edges,edgeSetAM-method", "edges,edgeSetNEL-method", "edges,multiGraph-method", "edgeSet-class", "edgeSetAM-class", "edgeSetNEL-class", "isDirected,edgeSet-method", "isDirected,multiGraph-method", "multiGraph-class", "nodes,edgeSetAM-method", "nodes,multiGraph-method", "numEdges,edgeSetAM-method", "numEdges,multiGraph-method", "numNodes,multiGraph-method", "show,edgeSet-method", "show,multiGraph-method" ] }, { "page": "MultiGraph-class", "title": "EXPERIMENTAL class \"MultiGraph\"", "topics": [ "edgeNames,MultiGraph-method", "edges,MultiGraph-method", "edgeSetIntersect0", "edgeSets", "edgeSets,MultiGraph-method", "edgeSetUnion0", "eweights", "extractFromTo", "extractFromTo,MultiGraph-method", "extractGraphAM", "extractGraphBAM", "graphIntersect,MultiGraph,MultiGraph-method", "graphUnion,MultiGraph,MultiGraph-method", "isDirected,DiEdgeSet-method", "isDirected,MultiGraph-method", "isDirected,UEdgeSet-method", "mgEdgeData", "mgEdgeData,MultiGraph,character,character,character,character-method", "mgEdgeData,MultiGraph,character,character,missing,character-method", "mgEdgeData,MultiGraph,character,missing,character,character-method", "mgEdgeData,MultiGraph,character,missing,missing,character-method", "mgEdgeData<-", "mgEdgeData<-,MultiGraph,character,character,character,character-method", "mgEdgeData<-,MultiGraph,character,character,missing,character-method", "mgEdgeData<-,MultiGraph,character,missing,character,character-method", "mgEdgeData<-,MultiGraph,character,missing,missing,character-method", "mgEdgeDataDefaults", "mgEdgeDataDefaults,MultiGraph,character,character-method", "mgEdgeDataDefaults,MultiGraph,character,missing-method", "mgEdgeDataDefaults<-", "mgEdgeDataDefaults<-,MultiGraph,character,character,ANY-method", "mgEdgeDataDefaults<-,MultiGraph,character,missing,list-method", "MultiGraph", "MultiGraph-class", "nodeData,MultiGraph,character,character-method", "nodeData,MultiGraph,character,missing-method", "nodeData,MultiGraph,missing,character-method", "nodeData,MultiGraph,missing,missing-method", "nodeData<-,MultiGraph,character,character-method", "nodeData<-,MultiGraph,missing,character-method", "nodeDataDefaults,MultiGraph,character-method", "nodeDataDefaults,MultiGraph,missing-method", "nodeDataDefaults<-,MultiGraph,character,ANY-method", "nodeDataDefaults<-,MultiGraph,missing,list-method", "nodes,MultiGraph-method", "numEdges,MGEdgeSet-method", "numEdges,MultiGraph-method", "numNodes,MultiGraph-method", "show,MultiGraph-method", "subsetEdgeSets", "ugraph,DiEdgeSet-method", "ugraph,MultiGraph-method", "ugraph,UEdgeSet-method" ] }, { "page": "nodeData-methods", "title": "Get and set attributes for the nodes of a graph object", "topics": [ "nodeData", "nodeData-methods", "nodeData<-", "nodeData<--methods" ] }, { "page": "nodeDataDefaults-methods", "title": "Get and set default attributes for the nodes of a graph", "topics": [ "nodeDataDefaults", "nodeDataDefaults-methods", "nodeDataDefaults<-", "nodeDataDefaults<--methods" ] }, { "page": "numNoEdges", "title": "Calculate the number of nodes that have an edge list of NULL", "topics": [ "numNoEdges" ] }, { "page": "pancrCaIni", "title": "A graph encoding parts of the pancreatic cancer initiation pathway", "topics": [ "pancrCaIni" ] }, { "page": "randomEGraph", "title": "Random Edge Graph", "topics": [ "randomEGraph" ] }, { "page": "randomGraph", "title": "Random Graph", "topics": [ "randomGraph" ] }, { "page": "randomNodeGraph", "title": "Generate Random Graph with Specified Degree Distribution", "topics": [ "randomNodeGraph" ] }, { "page": "removeEdge", "title": "removeEdge", "topics": [ "removeEdge" ] }, { "page": "removeNode", "title": "removeNode", "topics": [ "removeNode" ] }, { "page": "renderInfo-class", "title": "Class \"renderInfo\"", "topics": [ "edgeRenderInfo", "edgeRenderInfo<-", "graphRenderInfo", "graphRenderInfo<-", "nodeRenderInfo", "nodeRenderInfo<-", "parRenderInfo", "parRenderInfo<-", "renderInfo-class" ] }, { "page": "reverseEdgeDirections", "title": "Reverse the edges of a directed graph", "topics": [ "reverseEdgeDirections" ] }, { "page": "simpleEdge-class", "title": "Class \"simpleEdge\".", "topics": [ "simpleEdge-class" ] }, { "page": "standardLabeling", "title": "Standard labeling of edges with integers", "topics": [ "ftM2int", "int2ftM" ] }, { "page": "subGraph", "title": "Create a Subgraph", "topics": [ "subGraph", "subGraph,character,clusterGraph-method", "subGraph,character,distGraph-method", "subGraph,character,graphBAM-method", "subGraph,character,graphNEL-method", "subGraph,character,MultiGraph-method" ] }, { "page": "toDotR-methods", "title": "Methods for Function toDotR, using R to generate a dot serialization", "topics": [ "toDotR", "toDotR,graphNEL,character,list,list-method", "toDotR,graphNEL,character,missing,list-method", "toDotR,graphNEL,character,missing,missing-method", "toDotR,graphNEL,missing,character,missing-method", "toDotR,graphNEL,missing,list,list-method", "toDotR,graphNEL,missing,list,missing-method", "toDotR,graphNEL,missing,missing,list-method", "toDotR,graphNEL,missing,missing,missing-method" ] }, { "page": "toDotWithRI", "title": "Translate a graph to \"dot\" including rendering information", "topics": [ "toDotWithRI" ] }, { "page": "ugraph", "title": "Underlying Graph", "topics": [ "ugraph", "ugraph,graph-method" ] }, { "page": "validGraph", "title": "Test whether graph object is valid", "topics": [ "validGraph" ] }, { "page": "write.tlp", "title": "Write a graph object in a file in the Tulip format", "topics": [ "write.tlp" ] } ], "_rundeps": [ "BiocGenerics", "generics" ], "_vignettes": [ { "source": "graphAttributes.Rmd", "filename": "graphAttributes.html", "title": "Attributes for Graph Objects", "author": "Seth Falcon, Paul Villafuerte", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Getting edge attributes", "Setting edge attributes", "Node Attributes", "Default node attributes", "Getting and setting node attributes" ], "created": "2023-09-28 14:19:37", "modified": "2023-09-28 14:19:37", "commits": 1 }, { "source": "clusterGraph.Rmd", "filename": "clusterGraph.html", "title": "How To use the clusterGraph and distGraph classes", "author": "Robert Gentleman, Jeff Gentry, Seth Falcon, Paul Villafuerte", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "clusterGraph", "distGraph" ], "created": "2023-02-24 15:52:10", "modified": "2024-04-18 19:56:52", "commits": 2 }, { "source": "GraphClass.Rmd", "filename": "GraphClass.html", "title": "Graph Design", "author": "R. Gentleman, Elizabeth Whalen, W. Huber, S. Falcon, Halimat C. Atanda", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "The graph class", "Methods of graphs", "Some Details", "Representation of Edges", "Multi-graphs", "Methods", "Use Cases", "Bipartite Graphs" ], "created": "2022-10-28 02:43:41", "modified": "2022-10-28 02:43:41", "commits": 1 }, { "source": "MultiGraphClass.Rmd", "filename": "MultiGraphClass.html", "title": "graphBAM and MultiGraph classes", "author": "N. Gopalakrishnan, Halimat C. Atanda", "engine": "knitr::rmarkdown", "headings": [ "graphBAM class", "Introduction", "A simple graph represented using graphBAM class", "Mice gene interaction data for brain tissue (SAGE data)", "MultiGraphs", "A simple MultiGraph example", "MultiGraph representation of mice gene interaction data. (SAGE)" ], "created": "2022-12-07 01:29:27", "modified": "2022-12-07 01:29:27", "commits": 1 }, { "source": "graph.Rmd", "filename": "graph.html", "title": "How to use the graph package", "author": "Robert Gentleman, Seth Falcon, Jeff Gentry, Paul Shannon, Aliyu Atiku Mustapha", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Getting Started", "Some Algebraic Manipulations", "Random Graphs", "Some Graph Algorithms", "Special Types of Graphs", "Coercion", "Classes", "References" ], "created": "2023-03-27 20:24:26", "modified": "2024-04-18 19:56:52", "commits": 2 } ], "_score": 11.690452656378394, "_indexed": true, "_nocasepkg": "graph", "_universes": [ "bioc", "bioconductor-bot" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.91.0", "date": "2026-05-30T08:07:36.000Z", "distro": "noble", "arch": "aarch64", "commit": "ffac7de9cbac3adc7cd254d6a6c1c00359356b8f", "fileid": "cdb85aa199382bcc7b4f66c405b084d43694371611325e157eb450b85c7d9da4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678725383" }, { "r": "4.7.0", "os": "linux", "version": "1.91.0", "date": "2026-05-30T08:08:04.000Z", "distro": "noble", "arch": "x86_64", "commit": "ffac7de9cbac3adc7cd254d6a6c1c00359356b8f", "fileid": "f62eaf7a897321f99e8f2fa7eca44842cc87ff096ac1456ac7d30dfc75ed404c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678725383" }, { "r": "4.6.0", "os": "linux", "version": "1.91.0", "date": "2026-05-30T08:07:45.000Z", "distro": "noble", "arch": "aarch64", "commit": "ffac7de9cbac3adc7cd254d6a6c1c00359356b8f", "fileid": "4109f4192c3f7cfffacbf042198b3b72051a0452533c85082b5d919f43107a4f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678725383" }, { "r": "4.6.0", "os": "linux", "version": "1.91.0", "date": "2026-05-30T08:07:29.000Z", "distro": "noble", "arch": "x86_64", "commit": "ffac7de9cbac3adc7cd254d6a6c1c00359356b8f", "fileid": "3500c5e4148f8707842b513dfde4bcb1878aeeaa7294cd064dd18d0f3ba28c12", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678725383" }, { "r": "4.5.3", "os": "mac", "version": "1.91.0", "date": "2026-05-30T11:36:05.000Z", "arch": "aarch64", "commit": "ffac7de9cbac3adc7cd254d6a6c1c00359356b8f", "fileid": "b68aa2b22ff9c4af124550d2c17eded760245a99095b07b053b5377bc8fd01ab", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678725383" }, { "r": "4.5.3", "os": "mac", "version": "1.91.0", "date": "2026-05-30T08:07:52.000Z", "arch": "x86_64", "commit": "ffac7de9cbac3adc7cd254d6a6c1c00359356b8f", "fileid": "d93bfdb9b2247ee1bc1261c8de81b46c4fad0c65570e2b6ce54208c1ab0ec1d1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678725383" }, { "r": "4.6.0", "os": "mac", "version": "1.91.0", "date": "2026-05-30T11:36:04.000Z", "arch": "aarch64", "commit": "ffac7de9cbac3adc7cd254d6a6c1c00359356b8f", "fileid": "188535a3d997eceec092d4ef5b18edfc3f2ea9dadffb33a6b3ae60b84731ad87", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678725383" }, { "r": "4.6.0", "os": "mac", "version": "1.91.0", "date": "2026-05-30T08:08:13.000Z", "arch": "x86_64", "commit": "ffac7de9cbac3adc7cd254d6a6c1c00359356b8f", "fileid": "47981fc916ab78381ec4e73172ed996a6901424d828ad4f797a381faf7d88be3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678725383" }, { "r": "4.6.0", "os": "wasm", "version": "1.91.0", "date": "2026-05-30T08:07:01.000Z", "arch": "emscripten", "commit": "ffac7de9cbac3adc7cd254d6a6c1c00359356b8f", "fileid": "41265772aabc0a03178a812241768ee8cefe0088ab747e33508471688b3158e9", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678725383" }, { "r": "4.7.0", "os": "win", "version": "1.91.0", "date": "2026-05-30T08:06:19.000Z", "arch": "x86_64", "commit": "ffac7de9cbac3adc7cd254d6a6c1c00359356b8f", "fileid": "19fc551d270a5316ec880e8e976b44a993705896eb76b0328679dc67c7f146b9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678725383" }, { "r": "4.5.3", "os": "win", "version": "1.91.0", "date": "2026-05-30T08:06:29.000Z", "arch": "x86_64", "commit": "ffac7de9cbac3adc7cd254d6a6c1c00359356b8f", "fileid": "297faa71ac9a6214b546c78add0f37e56ae8e77ff27a6e7036af4a162718ea91", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678725383" }, { "r": "4.6.0", "os": "win", "version": "1.91.0", "date": "2026-05-30T08:06:27.000Z", "arch": "x86_64", "commit": "ffac7de9cbac3adc7cd254d6a6c1c00359356b8f", "fileid": "c937d15be663dafdc17a293d63d6e12dbb939a5db843b345f4ec17f7a93a2ddc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678725383" } ] }