{
  "_id": "6ac8c919de46216d5edd7301",
  "Package": "ComplexMap",
  "Title": "A Toolset for the Functional Analysis and Interactive\nVisualization of Protein Complex Data",
  "Version": "2.0.0",
  "Date": "2026-02-18",
  "Authors@R": "person(given = \"Qingzhou\",\nfamily = \"Zhang\",\nrole = c(\"aut\", \"cre\"),\nemail = \"zqzneptune@hotmail.com\",\ncomment = c(ORCID = \"0000-0001-9540-2624\"))",
  "Description": "Provides a comprehensive workflow for the quality control,\nrefinement, functional enrichment, and network-based analysis\nof protein complex datasets. ComplexMap allows for the\nquantitative evaluation of predicted complexes against a\nreference and provides an interactive Cytoscape.js-powered\nShiny explorer to navigate the functional landscape of a\nprotein complex map.",
  "URL": "https://zqzneptune.github.io/ComplexMap,\nhttps://github.com/zqzneptune/ComplexMap",
  "BugReports": "https://github.com/zqzneptune/ComplexMap/issues",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "BiocViews": "Software, Proteomics, NetworkAnalysis, Visualization,\nEnrichment, GeneSetEnrichment",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://zqzneptune.r-universe.dev",
  "Date/Publication": "2026-02-24 02:28:27 UTC",
  "RemoteUrl": "https://github.com/zqzneptune/ComplexMap",
  "RemoteRef": "HEAD",
  "RemoteSha": "83415bf695207de6f524601d6689030a23f7a9ee",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-09 10:24:55 UTC",
    "User": "root"
  },
  "Author": "Qingzhou Zhang [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-9540-2624>)",
  "Maintainer": "Qingzhou Zhang <zqzneptune@hotmail.com>",
  "_user": "zqzneptune",
  "_type": "src",
  "_file": "ComplexMap_2.0.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/c367fe9704f6e37b6429ae017a1d97b8f37e8d77a04ee9e182d944094d9d7e4d",
  "_filesize": 943610,
  "_sha256": "c367fe9704f6e37b6429ae017a1d97b8f37e8d77a04ee9e182d944094d9d7e4d",
  "_expires": "2027-01-17T10:59:35.000Z",
  "_created": "2026-10-09T10:24:55.000Z",
  "_published": "2026-10-09T10:59:37.319Z",
  "_buildurl": "https://github.com/r-universe/zqzneptune/actions/runs/37916879403",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 113777139235,
      "time": 245,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11610576436"
    },
    {
      "job": 113777139122,
      "time": 192,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11610376453"
    },
    {
      "job": 113777139226,
      "time": 214,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11611731769"
    },
    {
      "job": 113777139205,
      "time": 142,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11612420711"
    },
    {
      "job": 113775249680,
      "time": 330,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11610611502"
    },
    {
      "job": 113777139277,
      "time": 210,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11610372494"
    },
    {
      "job": 113777139017,
      "time": 107,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11610611893"
    },
    {
      "job": 113777139098,
      "time": 155,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11611061266"
    },
    {
      "job": 113777139037,
      "time": 151,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11610056581"
    }
  ],
  "_upstream": "https://github.com/zqzneptune/ComplexMap",
  "_commit": {
    "id": "83415bf695207de6f524601d6689030a23f7a9ee",
    "author": "zqzneptune <5545472+zqzneptune@users.noreply.github.com>",
    "committer": "zqzneptune <5545472+zqzneptune@users.noreply.github.com>",
    "message": "sidebar reset timer 10s\n",
    "time": 1771900107
  },
  "_maintainer": {
    "name": "Qingzhou Zhang",
    "email": "zqzneptune@hotmail.com",
    "login": "zqzneptune",
    "linkedin": "in/qingzhou-zhang-330094395",
    "twitter": "@QingzhouZ78967",
    "description": "Architecting Predictive Biology",
    "uuid": 5545472,
    "orcid": "0000-0001-9540-2624"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5",
      "role": "Depends"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "clue",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "future",
      "role": "Imports"
    },
    {
      "package": "future.apply",
      "role": "Imports"
    },
    {
      "package": "GO.db",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "msigdbr",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "reactome.db",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "colorspace",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "philentropy",
      "role": "Suggests"
    },
    {
      "package": "progressr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "zqzneptune",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-46",
      "n": 17
    },
    {
      "week": "2025-47",
      "n": 2
    },
    {
      "week": "2025-49",
      "n": 1
    },
    {
      "week": "2025-50",
      "n": 1
    },
    {
      "week": "2026-07",
      "n": 3
    },
    {
      "week": "2026-08",
      "n": 7
    },
    {
      "week": "2026-09",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "zqzneptune",
      "count": 33,
      "uuid": 5545472
    }
  ],
  "_userbio": {
    "uuid": 5545472,
    "type": "user",
    "name": "Qingzhou Zhang",
    "followers": 15,
    "description": "Architecting Predictive Biology"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ComplexMap"
  },
  "_devurl": "https://github.com/zqzneptune/complexmap",
  "_pkgdown": "https://zqzneptune.github.io/ComplexMap",
  "_searchresults": 6,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/ComplexMap.html",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_cranurl": false,
  "_exports": [
    "%>%",
    "benchmarkParameters",
    "buildComplexNetwork",
    "computeMapTopology",
    "createComplexMap",
    "evaluateComplexes",
    "explore",
    "exportNetwork",
    "generateNodeAttributes",
    "getEdgeTable",
    "getExampleGmt",
    "getGmtFromFile",
    "getGoGmt",
    "getMsigdbGmt",
    "getNodeTable",
    "getReactomeGmt",
    "pruneNetwork",
    "qcComplexList",
    "queryMap",
    "refineComplexList",
    "runComplexEnrichment",
    "runComplexMapApp",
    "scaleLayoutForCytoscape",
    "toCytoscapeJSON"
  ],
  "_datasets": [
    {
      "name": "demoComplexes",
      "title": "Example Protein Complex List",
      "object": "demoComplexes",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "referenceComplexes",
      "title": "Reference Protein Complex Set (CORUM)",
      "object": "referenceComplexes",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "benchmarkParameters",
      "title": "Benchmark Complex Refinement Parameters",
      "topics": [
        "benchmarkParameters"
      ]
    },
    {
      "page": "buildComplexNetwork",
      "title": "Build a Complex-Complex Interaction Network",
      "topics": [
        "buildComplexNetwork"
      ]
    },
    {
      "page": "computeMapTopology",
      "title": "Compute Network Topology and Layout Coordinates",
      "topics": [
        "computeMapTopology"
      ]
    },
    {
      "page": "createComplexMap",
      "title": "Create a Complete Complex Map Object",
      "topics": [
        "createComplexMap"
      ]
    },
    {
      "page": "demoComplexes",
      "title": "Example Protein Complex List",
      "topics": [
        "demoComplexes"
      ]
    },
    {
      "page": "evaluateComplexes",
      "title": "Evaluate Predicted Protein Complexes Against a Reference Set",
      "topics": [
        "evaluateComplexes"
      ]
    },
    {
      "page": "explore",
      "title": "Explore a ComplexMap Object Interactively",
      "topics": [
        "explore"
      ]
    },
    {
      "page": "exportNetwork",
      "title": "Export a ComplexMap Network for External Tools",
      "topics": [
        "exportNetwork"
      ]
    },
    {
      "page": "generateNodeAttributes",
      "title": "Generate Node Attributes for a Complex Network",
      "topics": [
        "generateNodeAttributes"
      ]
    },
    {
      "page": "getEdgeTable",
      "title": "Get the Edge Table from a ComplexMap Object",
      "topics": [
        "getEdgeTable"
      ]
    },
    {
      "page": "getExampleGmt",
      "title": "Get the Path to an Example GMT File",
      "topics": [
        "getExampleGmt"
      ]
    },
    {
      "page": "getGmtFromFile",
      "title": "Read a GMT File from a Local Path",
      "topics": [
        "getGmtFromFile"
      ]
    },
    {
      "page": "getGoGmt",
      "title": "Fetch Gene Ontology (GO) Gene Sets",
      "topics": [
        "getGoGmt"
      ]
    },
    {
      "page": "getMsigdbGmt",
      "title": "Fetch Gene Sets from MSigDB",
      "topics": [
        "getMsigdbGmt"
      ]
    },
    {
      "page": "getNodeTable",
      "title": "Get the Node Table from a ComplexMap Object",
      "topics": [
        "getNodeTable"
      ]
    },
    {
      "page": "getReactomeGmt",
      "title": "Fetch Reactome Pathway Gene Sets",
      "topics": [
        "getReactomeGmt"
      ]
    },
    {
      "page": "print.ComplexMap",
      "title": "Print Method for a ComplexMap Object",
      "topics": [
        "print.ComplexMap"
      ]
    },
    {
      "page": "pruneNetwork",
      "title": "Prune Network Edges Before Cytoscape Export",
      "topics": [
        "pruneNetwork"
      ]
    },
    {
      "page": "qcComplexList",
      "title": "Perform Quality Control on a List of Protein Complexes",
      "topics": [
        "qcComplexList"
      ]
    },
    {
      "page": "queryMap",
      "title": "Query a ComplexMap Object",
      "topics": [
        "queryMap"
      ]
    },
    {
      "page": "referenceComplexes",
      "title": "Reference Protein Complex Set (CORUM)",
      "topics": [
        "referenceComplexes"
      ]
    },
    {
      "page": "refineComplexList",
      "title": "Refine a List of Protein Complexes by Size and Redundancy",
      "topics": [
        "refineComplexList"
      ]
    },
    {
      "page": "runComplexEnrichment",
      "title": "Run Gene Set Enrichment Analysis on a List of Complexes",
      "topics": [
        "runComplexEnrichment"
      ]
    },
    {
      "page": "runComplexMapApp",
      "title": "Run the ComplexMap Interactive Explorer",
      "topics": [
        "runComplexMapApp"
      ]
    },
    {
      "page": "scaleLayoutForCytoscape",
      "title": "Scale Layout Coordinates for Cytoscape.js",
      "topics": [
        "scaleLayoutForCytoscape"
      ]
    },
    {
      "page": "toCytoscapeJSON",
      "title": "Export a ComplexMap Object to Cytoscape.js JSON",
      "topics": [
        "toCytoscapeJSON"
      ]
    }
  ],
  "_readme": "https://github.com/zqzneptune/ComplexMap/raw/HEAD/README.md",
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "assertthat",
    "babelgene",
    "base64enc",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "bslib",
    "cachem",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "commonmark",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "digest",
    "dplyr",
    "fastmap",
    "fontawesome",
    "fs",
    "future",
    "future.apply",
    "generics",
    "globals",
    "glue",
    "GO.db",
    "htmltools",
    "httpuv",
    "httr",
    "igraph",
    "IRanges",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "later",
    "lattice",
    "lifecycle",
    "listenv",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "msigdbr",
    "openssl",
    "otel",
    "parallelly",
    "pillar",
    "pkgconfig",
    "png",
    "promises",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "reactome.db",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "sass",
    "Seqinfo",
    "shiny",
    "sourcetools",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "xtable",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "vignette_01-prep-input.Rmd",
      "filename": "vignette_01-prep-input.html",
      "title": "Preparing Your Input Data ",
      "author": "Qingzhou Zhang",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The ComplexMap Philosophy: Identifier Matching",
        "Preparing Functional Gene Sets (GMT)",
        "Method 1: From a User-Provided Local File",
        "Method 2: From the Molecular Signatures Database (MSigDB)",
        "Method 3: From Gene Ontology (GO) via Bioconductor",
        "Method 4: From Reactome Pathways via Bioconductor"
      ],
      "created": "2025-11-11 21:13:37",
      "modified": "2025-12-03 12:30:07",
      "commits": 2
    },
    {
      "source": "vignette_02-workflow.Rmd",
      "filename": "vignette_02-workflow.html",
      "title": "Start a Typical Workflow ",
      "author": "Qingzhou Zhang",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Step 1: Loading Data",
        "Step 2: Running the Main Workflow",
        "The Systems Biology Dashboard",
        "Step 3: Exploring and Querying",
        "3.1 Targeted Querying",
        "3.2 Accessing Tables",
        "Step 4: Interactive Visualization",
        "Step 5: Exporting to External Tools",
        "Conclusion"
      ],
      "created": "2025-11-11 21:13:37",
      "modified": "2026-02-19 14:49:15",
      "commits": 5
    }
  ],
  "_score": 3.845098040014257,
  "_indexed": true,
  "_nocasepkg": "complexmap",
  "_universes": [
    "zqzneptune"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.0.0",
      "date": "2026-10-09T10:28:58.000Z",
      "distro": "resolute",
      "commit": "83415bf695207de6f524601d6689030a23f7a9ee",
      "fileid": "https://r2.ropensci.org/c1f3036167d81e3460a15dd2e3cdc9f1e02fa9bbfe2d0a22fc49889aae7a2162",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/zqzneptune/actions/runs/37916879403"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.0.0",
      "date": "2026-10-09T10:28:12.000Z",
      "distro": "resolute",
      "commit": "83415bf695207de6f524601d6689030a23f7a9ee",
      "fileid": "https://r2.ropensci.org/44c65dd00d1d8c03248ecc3f84273a8fa11814abe04a8e8fd03c675d347539a0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/zqzneptune/actions/runs/37916879403"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.0.0",
      "date": "2026-10-09T10:58:25.000Z",
      "commit": "83415bf695207de6f524601d6689030a23f7a9ee",
      "fileid": "https://r2.ropensci.org/e5069172a6e019680b6bb7ab469a2f72f55823a924a08228fb7861324b2f7d08",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/zqzneptune/actions/runs/37916879403"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.0.0",
      "date": "2026-10-09T10:58:04.000Z",
      "commit": "83415bf695207de6f524601d6689030a23f7a9ee",
      "fileid": "https://r2.ropensci.org/4446a2a9104394bed53f8ed40a06a45c3313bca71ccda6144528107e19e515be",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/zqzneptune/actions/runs/37916879403"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.0.0",
      "date": "2026-10-09T10:28:44.000Z",
      "commit": "83415bf695207de6f524601d6689030a23f7a9ee",
      "fileid": "https://r2.ropensci.org/e0603e43c960076e37f60d5390b7ecb497e83490e8fe9cf70996edb55feba4f6",
      "status": "success",
      "buildurl": "https://github.com/r-universe/zqzneptune/actions/runs/37916879403"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.0.0",
      "date": "2026-10-09T10:26:44.000Z",
      "commit": "83415bf695207de6f524601d6689030a23f7a9ee",
      "fileid": "https://r2.ropensci.org/6dbd50c533f24e89266839cad00918cf56f9e6d93e7421b8a38c15f486b09e36",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/zqzneptune/actions/runs/37916879403"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.0.0",
      "date": "2026-10-09T10:27:27.000Z",
      "commit": "83415bf695207de6f524601d6689030a23f7a9ee",
      "fileid": "https://r2.ropensci.org/477c40ebec6ab704794cb8c44ea113ace1db10126fc1f1a37192875f51bbcc03",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/zqzneptune/actions/runs/37916879403"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.0.0",
      "date": "2026-10-09T10:27:18.000Z",
      "commit": "83415bf695207de6f524601d6689030a23f7a9ee",
      "fileid": "https://r2.ropensci.org/be53dcd54cd7e9c443224334751abaf7b4e7185a55486fa30a83518dd351a6df",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/zqzneptune/actions/runs/37916879403"
    }
  ]
}