{
  "_id": "6a1fdd34b401979e734384c4",
  "Package": "RCX",
  "Type": "Package",
  "Title": "R package implementing the Cytoscape Exchange (CX) format",
  "Version": "1.17.0",
  "Authors@R": "person(\"Florian\", \"Auer\", role = c(\"aut\",\"cre\"), \nemail=\"florian.auer@informatik.uni-augsburg.de\",\ncomment = c(ORCID = \"0000-0002-5320-8900\"))",
  "Description": "Create, handle, validate, visualize and convert networks\nin the Cytoscape exchange (CX) format to standard data types\nand objects. The package also provides conversion to and from\nobjects of iGraph and graphNEL. The CX format is also used by\nthe NDEx platform, a online commons for biological networks,\nand the network visualization software Cytocape.",
  "License": "MIT + file LICENSE",
  "RoxygenNote": "7.3.2",
  "Roxygen": "list(markdown = TRUE)",
  "biocViews": "Pathways, DataImport, Network",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "URL": "https://github.com/frankkramer-lab/RCX",
  "BugReports": "https://github.com/frankkramer-lab/RCX/issues",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:57:41 UTC",
  "RemoteUrl": "https://github.com/bioc/RCX",
  "RemoteRef": "HEAD",
  "RemoteSha": "ae8457eaefc4f1cc678139aa28039894f0e8e01d",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-03 07:48:17 UTC",
    "User": "root"
  },
  "Author": "Florian Auer [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-5320-8900>)",
  "Maintainer": "Florian Auer <florian.auer@informatik.uni-augsburg.de>",
  "MD5sum": "d65604db783d0d9f0d783d84efdc9268",
  "_user": "bioc",
  "_type": "src",
  "_file": "RCX_1.17.0.tar.gz",
  "_fileid": "04c9daebafc411846a14c64449f61cfdf5dc50c23b05cd98708fd3abadbd3fc6",
  "_filesize": 4312444,
  "_sha256": "04c9daebafc411846a14c64449f61cfdf5dc50c23b05cd98708fd3abadbd3fc6",
  "_created": "2026-06-03T07:48:17.000Z",
  "_published": "2026-06-03T07:52:20.450Z",
  "_jobs": [
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  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26870979179",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/RCX",
  "_commit": {
    "id": "ae8457eaefc4f1cc678139aa28039894f0e8e01d",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381061
  },
  "_maintainer": {
    "name": "Florian Auer",
    "email": "florian.auer@informatik.uni-augsburg.de",
    "login": "florian-j-auer",
    "description": "",
    "uuid": 20659040,
    "orcid": "0000-0002-5320-8900"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2.0",
      "role": "Depends"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "base64enc",
      "role": "Suggests"
    },
    {
      "package": "graph",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-36",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-04",
      "n": 2
    },
    {
      "week": "2026-12",
      "n": 2
    },
    {
      "week": "2026-18",
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    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.17.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.16.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "pathways",
    "dataimport",
    "network"
  ],
  "_stars": 8,
  "_contributors": [
    {
      "user": "florian-j-auer",
      "count": 37,
      "uuid": 20659040
    },
    {
      "user": "jwokaty",
      "count": 13,
      "uuid": 1744257
    },
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      "uuid": 2746443
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 338,
    "source": "https://www.bioconductor.org/packages/stats/bioc/RCX"
  },
  "_devurl": "https://github.com/frankkramer-lab/rcx",
  "_searchresults": 21,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/RCX.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/frankkramer-lab/rcx",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    ".markAttributeColumn<-",
    ".markRefColumn<-",
    "aspectClass2Name",
    "aspectClasses",
    "aspectName2Class",
    "countElements",
    "createCartesianLayout",
    "createCyGroups",
    "createCyHiddenAttributes",
    "createCyNetworkRelations",
    "createCySubNetworks",
    "createCyTableColumn",
    "createCyVisualProperties",
    "createCyVisualProperty",
    "createCyVisualPropertyDependencies",
    "createCyVisualPropertyMappings",
    "createCyVisualPropertyProperties",
    "createEdgeAttributes",
    "createEdges",
    "createNetworkAttributes",
    "createNodeAttributes",
    "createNodes",
    "createRCX",
    "fromGraphNEL",
    "fromIgraph",
    "getAspectClasses",
    "getCyVisualProperty",
    "hasIds",
    "idProperty",
    "jsonToRCX",
    "maxId",
    "parseJSON",
    "processCX",
    "rcxToJson",
    "readCX",
    "readJSON",
    "referredBy",
    "refersTo",
    "setExtension",
    "subAspectClasses",
    "toCX",
    "toGraphNEL",
    "toIgraph",
    "updateAspectClasses",
    "updateCartesianLayout",
    "updateCyGroups",
    "updateCyHiddenAttributes",
    "updateCyNetworkRelations",
    "updateCySubNetworks",
    "updateCyTableColumn",
    "updateCyVisualProperties",
    "updateCyVisualProperty",
    "updateEdgeAttributes",
    "updateEdges",
    "updateMetaData",
    "updateMetaDataProperties",
    "updateNetworkAttributes",
    "updateNodeAttributes",
    "updateNodes",
    "validate",
    "visualize",
    "writeCX",
    "writeHTML"
  ],
  "_help": [
    {
      "page": "aspectClasses",
      "title": "aspectClasses and subAspectClasses",
      "topics": [
        "aspectClasses",
        "getAspectClasses",
        "subAspectClasses",
        "updateAspectClasses"
      ]
    },
    {
      "page": "CartesianLayout",
      "title": "Cartesian layout",
      "topics": [
        "CartesianLayout",
        "createCartesianLayout"
      ]
    },
    {
      "page": "Convert-Names-and-Classes",
      "title": "Convert aspect class name to RCX accession",
      "topics": [
        "aspectClass2Name",
        "aspectName2Class",
        "Convert-Names-and-Classes"
      ]
    },
    {
      "page": "countElements",
      "title": "Number of elements in aspect",
      "topics": [
        "countElements",
        "countElements.CyVisualPropertiesAspect",
        "countElements.default",
        "countElements.MetaDataAspect",
        "countElements.RCX"
      ]
    },
    {
      "page": "custom-print",
      "title": "Print functions for RCX and aspect classes",
      "topics": [
        "custom-print",
        "print.CartesianLayoutAspect",
        "print.CyGroupsAspect",
        "print.CyHiddenAttributesAspect",
        "print.CyNetworkRelationsAspect",
        "print.CySubNetworksAspect",
        "print.CyTableColumnAspect",
        "print.CyVisualPropertiesAspect",
        "print.CyVisualProperty",
        "print.CyVisualPropertyDependencies",
        "print.CyVisualPropertyMappings",
        "print.CyVisualPropertyProperties",
        "print.EdgeAttributesAspect",
        "print.EdgesAspect",
        "print.MetaDataAspect",
        "print.NetworkAttributesAspect",
        "print.NodeAttributesAspect",
        "print.NodesAspect",
        "print.RCX"
      ]
    },
    {
      "page": "CyGroups",
      "title": "Cytoscape Groups",
      "topics": [
        "createCyGroups",
        "CyGroups"
      ]
    },
    {
      "page": "CyHiddenAttributes",
      "title": "Cytoscape hidden attributes",
      "topics": [
        "createCyHiddenAttributes",
        "CyHiddenAttributes"
      ]
    },
    {
      "page": "CyNetworkRelations",
      "title": "Cytoscape network relations",
      "topics": [
        "createCyNetworkRelations",
        "CyNetworkRelations"
      ]
    },
    {
      "page": "CySubNetworks",
      "title": "Cytoscape subnetworks",
      "topics": [
        "createCySubNetworks",
        "CySubNetworks"
      ]
    },
    {
      "page": "CyTableColumn",
      "title": "Cytoscape table column properties",
      "topics": [
        "createCyTableColumn",
        "CyTableColumn"
      ]
    },
    {
      "page": "CyVisualProperties",
      "title": "Cytoscape visual properties (aspect)",
      "topics": [
        "createCyVisualProperties",
        "CyVisualProperties"
      ]
    },
    {
      "page": "CyVisualProperty",
      "title": "Cytoscape visual property (object used in CyVisualProperties aspect)",
      "topics": [
        "createCyVisualProperty",
        "CyVisualProperty"
      ]
    },
    {
      "page": "CyVisualPropertyDependencies",
      "title": "Create a object for dependency of Cytoscape Visual Properties (object used in CyVisualProperty)",
      "topics": [
        "createCyVisualPropertyDependencies",
        "CyVisualPropertyDependencies"
      ]
    },
    {
      "page": "CyVisualPropertyMappings",
      "title": "Create an object for mappings of Cytoscape Visual Properties (object used in CyVisualProperty)",
      "topics": [
        "createCyVisualPropertyMappings",
        "CyVisualPropertyMappings"
      ]
    },
    {
      "page": "CyVisualPropertyProperties",
      "title": "Create a object for properties of Cytoscape Visual Properties (object used in CyVisualProperty)",
      "topics": [
        "createCyVisualPropertyProperties",
        "CyVisualPropertyProperties"
      ]
    },
    {
      "page": "EdgeAttributes",
      "title": "Edge attributes",
      "topics": [
        "createEdgeAttributes",
        "EdgeAttributes"
      ]
    },
    {
      "page": "Edges",
      "title": "Edges",
      "topics": [
        "createEdges",
        "Edges"
      ]
    },
    {
      "page": "getCyVisualProperty",
      "title": "Get a Cytoscape visual property (object used in CyVisualProperties aspect) by appliesTo and view",
      "topics": [
        "getCyVisualProperty"
      ]
    },
    {
      "page": "graphNEL",
      "title": "Convert an RCX object from and to an graphNEL object",
      "topics": [
        "fromGraphNEL",
        "graphNEL",
        "toGraphNEL"
      ]
    },
    {
      "page": "hasIds",
      "title": "IDs of an aspect",
      "topics": [
        "hasIds",
        "hasIds.CyGroupsAspect",
        "hasIds.CySubNetworksAspect",
        "hasIds.default",
        "hasIds.EdgesAspect",
        "hasIds.NodesAspect"
      ]
    },
    {
      "page": "idProperty",
      "title": "Name of the property of an aspect that is an ID",
      "topics": [
        "idProperty",
        "idProperty.CyGroupsAspect",
        "idProperty.CySubNetworksAspect",
        "idProperty.default",
        "idProperty.EdgesAspect",
        "idProperty.NodesAspect"
      ]
    },
    {
      "page": "Igraph",
      "title": "Convert an RCX object from and to an igraph object",
      "topics": [
        "fromIgraph",
        "Igraph",
        "toIgraph"
      ]
    },
    {
      "page": "jsonToRCX",
      "title": "Convert parsed JSON aspects to RCX",
      "topics": [
        "jsonToRCX",
        "jsonToRCX.cartesianLayout",
        "jsonToRCX.cyGroups",
        "jsonToRCX.cyHiddenAttributes",
        "jsonToRCX.cyNetworkRelations",
        "jsonToRCX.cySubNetworks",
        "jsonToRCX.cyTableColumn",
        "jsonToRCX.cyVisualProperties",
        "jsonToRCX.default",
        "jsonToRCX.edgeAttributes",
        "jsonToRCX.edges",
        "jsonToRCX.metaData",
        "jsonToRCX.networkAttributes",
        "jsonToRCX.nodeAttributes",
        "jsonToRCX.nodes",
        "jsonToRCX.numberVerification",
        "jsonToRCX.status"
      ]
    },
    {
      "page": "maxId",
      "title": "Highest ID of an aspect",
      "topics": [
        "maxId",
        "maxId.default",
        "maxId.RCX"
      ]
    },
    {
      "page": "Meta-data",
      "title": "Update RCX meta-data",
      "topics": [
        "Meta-data",
        "updateMetaData",
        "updateMetaData.default",
        "updateMetaData.RCX"
      ]
    },
    {
      "page": "NetworkAttributes",
      "title": "Network attributes",
      "topics": [
        "createNetworkAttributes",
        "NetworkAttributes"
      ]
    },
    {
      "page": "NodeAttributes",
      "title": "Node attributes",
      "topics": [
        "createNodeAttributes",
        "NodeAttributes"
      ]
    },
    {
      "page": "Nodes",
      "title": "Nodes",
      "topics": [
        "createNodes",
        "Nodes"
      ]
    },
    {
      "page": "RCX-object",
      "title": "Create an RCX object from aspects",
      "topics": [
        "createRCX",
        "RCX-object"
      ]
    },
    {
      "page": "rcxToJson",
      "title": "Convert RCX aspects to JSON",
      "topics": [
        "rcxToJson",
        "rcxToJson.CartesianLayoutAspect",
        "rcxToJson.CyGroupsAspect",
        "rcxToJson.CyHiddenAttributesAspect",
        "rcxToJson.CyNetworkRelationsAspect",
        "rcxToJson.CySubNetworksAspect",
        "rcxToJson.CyTableColumnAspect",
        "rcxToJson.CyVisualPropertiesAspect",
        "rcxToJson.CyVisualProperty",
        "rcxToJson.CyVisualPropertyDependencies",
        "rcxToJson.CyVisualPropertyMappings",
        "rcxToJson.CyVisualPropertyProperties",
        "rcxToJson.default",
        "rcxToJson.EdgeAttributesAspect",
        "rcxToJson.EdgesAspect",
        "rcxToJson.MetaDataAspect",
        "rcxToJson.NetworkAttributesAspect",
        "rcxToJson.NodeAttributesAspect",
        "rcxToJson.NodesAspect"
      ]
    },
    {
      "page": "readCX",
      "title": "Read CX from file, parse the JSON and convert it to an RCX object",
      "topics": [
        "parseJSON",
        "processCX",
        "readCX",
        "readJSON"
      ]
    },
    {
      "page": "referredBy",
      "title": "List the aspects that are refered by an other aspect",
      "topics": [
        "referredBy"
      ]
    },
    {
      "page": "refersTo",
      "title": "Name of the property of an aspect that is an ID",
      "topics": [
        "refersTo",
        "refersTo.CartesianLayoutAspect",
        "refersTo.CyGroupsAspect",
        "refersTo.CySubNetworksAspect",
        "refersTo.CyVisualPropertiesAspect",
        "refersTo.default",
        "refersTo.EdgeAttributesAspect",
        "refersTo.EdgesAspect",
        "refersTo.NodeAttributesAspect"
      ]
    },
    {
      "page": "setExtension",
      "title": "Set or register an RCX extension",
      "topics": [
        "setExtension"
      ]
    },
    {
      "page": "summary",
      "title": "RCX and aspect summary",
      "topics": [
        "summary",
        "summary.AspectAttributeColumn",
        "summary.AspectIdColumn",
        "summary.AspectListLengthColumn",
        "summary.AspectRefColumn",
        "summary.AspectReqRefColumn",
        "summary.AspectValueColumn",
        "summary.CartesianLayoutAspect",
        "summary.CyGroupsAspect",
        "summary.CyHiddenAttributesAspect",
        "summary.CyNetworkRelationsAspect",
        "summary.CySubNetworksAspect",
        "summary.CyTableColumnAspect",
        "summary.CyVisualPropertiesAspect",
        "summary.CyVisualProperty",
        "summary.EdgeAttributesAspect",
        "summary.EdgesAspect",
        "summary.MetaDataAspect",
        "summary.NetworkAttributesAspect",
        "summary.NodeAttributesAspect",
        "summary.NodesAspect",
        "summary.RCX"
      ]
    },
    {
      "page": "toCX",
      "title": "Convert an RCX object to CX (JSON)",
      "topics": [
        "toCX"
      ]
    },
    {
      "page": "updateCartesianLayout",
      "title": "Update Cartesian Layouts",
      "topics": [
        "updateCartesianLayout",
        "updateCartesianLayout.CartesianLayoutAspect",
        "updateCartesianLayout.RCX"
      ]
    },
    {
      "page": "updateCyGroups",
      "title": "Update Cytoscape Groups",
      "topics": [
        "updateCyGroups",
        "updateCyGroups.CyGroupsAspect",
        "updateCyGroups.RCX"
      ]
    },
    {
      "page": "updateCyHiddenAttributes",
      "title": "Update Cytoscape hidden attributes",
      "topics": [
        "updateCyHiddenAttributes",
        "updateCyHiddenAttributes.CyHiddenAttributesAspect",
        "updateCyHiddenAttributes.RCX"
      ]
    },
    {
      "page": "updateCyNetworkRelations",
      "title": "Update Cytoscape network relations",
      "topics": [
        "updateCyNetworkRelations",
        "updateCyNetworkRelations.CyNetworkRelationsAspect",
        "updateCyNetworkRelations.RCX"
      ]
    },
    {
      "page": "updateCySubNetworks",
      "title": "Update Cytoscape subnetworks",
      "topics": [
        "updateCySubNetworks",
        "updateCySubNetworks.CySubNetworksAspect",
        "updateCySubNetworks.RCX"
      ]
    },
    {
      "page": "updateCyTableColumn",
      "title": "Update Cytoscape table column properties",
      "topics": [
        "updateCyTableColumn",
        "updateCyTableColumn.CyTableColumnAspect",
        "updateCyTableColumn.RCX"
      ]
    },
    {
      "page": "updateCyVisualProperties",
      "title": "Update Cytoscape Visual Properties (aspect)",
      "topics": [
        "updateCyVisualProperties",
        "updateCyVisualProperties.CyVisualPropertiesAspect",
        "updateCyVisualProperties.RCX"
      ]
    },
    {
      "page": "updateCyVisualProperty",
      "title": "Update Cytoscape Visual Property objects and sub-objects (used in CyVisualProperties aspect)",
      "topics": [
        "updateCyVisualProperty",
        "updateCyVisualProperty.CyVisualProperty",
        "updateCyVisualProperty.CyVisualPropertyDependencies",
        "updateCyVisualProperty.CyVisualPropertyMappings",
        "updateCyVisualProperty.CyVisualPropertyProperties"
      ]
    },
    {
      "page": "updateEdgeAttributes",
      "title": "Update edge attributes",
      "topics": [
        "updateEdgeAttributes",
        "updateEdgeAttributes.EdgeAttributesAspect",
        "updateEdgeAttributes.RCX"
      ]
    },
    {
      "page": "updateEdges",
      "title": "Update edges",
      "topics": [
        "updateEdges",
        "updateEdges.EdgesAspect",
        "updateEdges.RCX"
      ]
    },
    {
      "page": "updateMetaDataProperties",
      "title": "Update meta-data properties",
      "topics": [
        "updateMetaDataProperties"
      ]
    },
    {
      "page": "updateNetworkAttributes",
      "title": "Update network attributes",
      "topics": [
        "updateNetworkAttributes",
        "updateNetworkAttributes.NetworkAttributesAspect",
        "updateNetworkAttributes.RCX"
      ]
    },
    {
      "page": "updateNodeAttributes",
      "title": "Update node attributes",
      "topics": [
        "updateNodeAttributes",
        "updateNodeAttributes.NodeAttributesAspect",
        "updateNodeAttributes.RCX"
      ]
    },
    {
      "page": "updateNodes",
      "title": "Update nodes",
      "topics": [
        "updateNodes",
        "updateNodes.NodesAspect",
        "updateNodes.RCX"
      ]
    },
    {
      "page": "validate",
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