{
  "_id": "6ab6c54399f7aa8c6aa2f2a5",
  "Package": "WayFindR",
  "Version": "0.7.1",
  "Date": "2026-09-25",
  "Title": "Computing Graph Structures on WikiPathways",
  "Authors@R": "c(person(\"Kevin R.\", \"Coombes\", role = c(\"aut\", \"cre\"),\nemail = \"krc@silicovore.com\"),\nperson(\"Polina\", \"Bombina\", role = c(\"aut\"),\nemail = \"pbombina@augusta.edu\"))",
  "Description": "Converts pathways from 'WikiPathways' GPML format or\n'KEGG' KGML format into 'igraph' objects. Includes tools to\nfind all cycles in the resulting graphs and determine which\nones involve negative feedback (inhibition). See\n<doi:10.1093/nargab/lqag051>.",
  "License": "Artistic-2.0",
  "URL": "http://silicovore.com/OOMPA/cytangle.html",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-25 18:56:20 UTC",
    "User": "root"
  },
  "Author": "Kevin R. Coombes [aut, cre], Polina Bombina [aut]",
  "Maintainer": "Kevin R. Coombes <krc@silicovore.com>",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-09-25 15:20:02 UTC",
  "RemoteUrl": "https://github.com/cran/WayFindR",
  "RemoteRef": "HEAD",
  "RemoteSha": "930823d38b94508b774cdd6bb33bfce82b9d4c79",
  "_user": "cran",
  "_type": "src",
  "_file": "WayFindR_0.7.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/fc8ea85727e73a2876fad4a8a3c01613ebc788527949499ea0f5d4d803eeab5e",
  "_filesize": 3746886,
  "_sha256": "fc8ea85727e73a2876fad4a8a3c01613ebc788527949499ea0f5d4d803eeab5e",
  "_expires": "2027-01-03T19:02:24.000Z",
  "_created": "2026-09-25T18:56:20.000Z",
  "_published": "2026-09-25T19:02:27.054Z",
  "_jobs": [
    {
      "job": 108208714063,
      "time": 302,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10882995043"
    },
    {
      "job": 108208714031,
      "time": 308,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10882348322"
    },
    {
      "job": 108206969735,
      "time": 304,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10881619388"
    },
    {
      "job": 108208713955,
      "time": 181,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10882382816"
    },
    {
      "job": 108208714152,
      "time": 231,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10882652890"
    },
    {
      "job": 108208714070,
      "time": 235,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10881969593"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/36176068449",
  "_status": "success",
  "_upstream": "https://github.com/cran/WayFindR",
  "_commit": {
    "id": "930823d38b94508b774cdd6bb33bfce82b9d4c79",
    "author": "Kevin R. Coombes <krc@silicovore.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.7.1\n",
    "time": 1790349602
  },
  "_maintainer": {
    "name": "Kevin R. Coombes",
    "email": "krc@silicovore.com"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "XML",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "KEGGREST",
      "role": "Imports"
    },
    {
      "package": "DescTools",
      "role": "Imports"
    },
    {
      "package": "Rgraphviz",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "Polychrome",
      "role": "Suggests"
    },
    {
      "package": "AnnotationDbi",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-45",
      "n": 1
    },
    {
      "week": "2026-02",
      "n": 1
    },
    {
      "week": "2026-39",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "0.5.0",
      "date": "2025-11-05"
    },
    {
      "name": "0.7.0",
      "date": "2026-01-08"
    },
    {
      "name": "0.7.1",
      "date": "2026-09-25"
    }
  ],
  "_stars": 0,
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "followers": 630,
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 454,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/WayFindR"
  },
  "_searchresults": 13,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/WayFindR.html"
  ],
  "_realowner": "cran",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.2",
      "date": "2024-04-10"
    },
    {
      "version": "0.3.1",
      "date": "2025-04-09"
    },
    {
      "version": "0.4.1",
      "date": "2025-09-20"
    },
    {
      "version": "0.5.0",
      "date": "2025-11-05"
    },
    {
      "version": "0.7.0",
      "date": "2026-01-08"
    },
    {
      "version": "0.7.1",
      "date": "2026-09-25"
    }
  ],
  "_exports": [
    "as.graphNEL",
    "collectAnchors",
    "collectEdges",
    "collectEntries",
    "collectGroups",
    "collectLabels",
    "collectNodes",
    "collectReactions",
    "collectRelations",
    "collectShapes",
    "cycleSubgraph",
    "discoverCycles",
    "edgeLegend",
    "findCycles",
    "GPMLtoIgraph",
    "interpretCycle",
    "KGMLtoIgraph",
    "nodeLegend"
  ],
  "_datasets": [
    {
      "name": "edgeColors",
      "title": "GPML GraphingR Data",
      "object": "edgeColors",
      "file": "edgeColors.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "edgeTypes",
      "title": "GPML GraphingR Data",
      "object": "edgeTypes",
      "file": "edgeTypes.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "nodeColors",
      "title": "GPML GraphingR Data",
      "object": "nodeColors",
      "file": "nodeColors.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "nodeShapes",
      "title": "GPML GraphingR Data",
      "object": "nodeShapes",
      "file": "nodeShapes.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "11-coerce",
      "title": "Convert igraph object to Ragraph",
      "topics": [
        "as.graphNEL"
      ]
    },
    {
      "page": "04-cycles",
      "title": "Finding Cycles in Biological Pathways",
      "topics": [
        "cycleSubgraph",
        "discoverCycles",
        "findCycles",
        "gpml-cycles",
        "interpretCycle"
      ]
    },
    {
      "page": "01-data",
      "title": "GPML GraphingR Data",
      "topics": [
        "edgeColors",
        "edgeTypes",
        "gpml-data",
        "nodeColors",
        "nodeShapes"
      ]
    },
    {
      "page": "02-util",
      "title": "Utility Functions to Parse GPML FIles",
      "topics": [
        "collectAnchors",
        "collectEdges",
        "collectGroups",
        "collectLabels",
        "collectNodes",
        "collectShapes",
        "gpml-utility"
      ]
    },
    {
      "page": "10-kgml-util",
      "title": "Utility Functions to Parse KGML FIles",
      "topics": [
        "collectEntries",
        "collectReactions",
        "collectRelations",
        "kgml-utility"
      ]
    },
    {
      "page": "03-main",
      "title": "Converting GPML FIles to Igraph Objects",
      "topics": [
        "edgeLegend",
        "GPMLtoIgraph",
        "KGMLtoIgraph",
        "nodeLegend"
      ]
    }
  ],
  "_rundeps": [
    "askpass",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "boot",
    "cellranger",
    "class",
    "cli",
    "clipr",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DescTools",
    "e1071",
    "Exact",
    "expm",
    "forcats",
    "fs",
    "generics",
    "gld",
    "glue",
    "graph",
    "haven",
    "hms",
    "httr",
    "igraph",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lattice",
    "lifecycle",
    "lmom",
    "magrittr",
    "MASS",
    "Matrix",
    "mime",
    "mvtnorm",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "proxy",
    "R6",
    "Rcpp",
    "readr",
    "readxl",
    "rematch",
    "Rgraphviz",
    "rlang",
    "rootSolve",
    "rstudioapi",
    "S4Vectors",
    "Seqinfo",
    "sys",
    "tibble",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "withr",
    "XML",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "WayFindR_metrics.Rmd",
      "filename": "WayFindR_metrics.html",
      "title": "WayFindR: Computing Graph Metrics on WikiPathways",
      "author": "Polina Bombina and Kevin R. Coombes",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Data Preparation",
        "Computing graph metrics",
        "Degrees and Hubs"
      ],
      "created": "2025-04-09 07:40:17",
      "modified": "2025-04-09 07:40:17",
      "commits": 1
    },
    {
      "source": "WayFindR_getStarted.Rmd",
      "filename": "WayFindR_getStarted.html",
      "title": "WayFindR: Creating Graph Structures From WikiPathways Files",
      "author": "Polina Bombina and Kevin R. Coombes",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Retrieving data structure from GPML file",
        "Edges",
        "Nodes",
        "Groups",
        "Anchors",
        "Converting Pathways into igraph objects",
        "Bundling the Process",
        "Finding cycles"
      ],
      "created": "2024-04-11 02:34:37",
      "modified": "2026-01-08 22:20:02",
      "commits": 4
    },
    {
      "source": "WayFindR_plots.Rmd",
      "filename": "WayFindR_plots.html",
      "title": "WayFindR: Displaying WikiPathways",
      "author": "Polina Bombina and Kevin R. Coombes",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Data Preparation",
        "Plots"
      ],
      "created": "2025-04-09 07:40:17",
      "modified": "2025-04-09 07:40:17",
      "commits": 1
    }
  ],
  "_score": 3.0681858617461617,
  "_indexed": true,
  "_nocasepkg": "wayfindr",
  "_universes": [
    "cran"
  ],
  "_previous": "0.7.0",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.7.1",
      "date": "2026-09-25T18:59:26.000Z",
      "distro": "resolute",
      "commit": "930823d38b94508b774cdd6bb33bfce82b9d4c79",
      "fileid": "https://r2.ropensci.org/d2bee991bf018402757a8b39b52b391f9b2183cfff5f1527b016a468015cff80",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/36176068449"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.7.1",
      "date": "2026-09-25T18:59:28.000Z",
      "distro": "resolute",
      "commit": "930823d38b94508b774cdd6bb33bfce82b9d4c79",
      "fileid": "https://r2.ropensci.org/e133300463f9d04ba21fac731c6d96379f8869d228c415ecb65da4cd41f30e05",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/36176068449"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.7.1",
      "date": "2026-09-25T18:59:48.000Z",
      "commit": "930823d38b94508b774cdd6bb33bfce82b9d4c79",
      "fileid": "https://r2.ropensci.org/f06f7898b7be47d7c0fac3fa5c5a0258facd8173992dcba3865dc2a5912c44f0",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/36176068449"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.7.1",
      "date": "2026-09-25T18:58:21.000Z",
      "commit": "930823d38b94508b774cdd6bb33bfce82b9d4c79",
      "fileid": "https://r2.ropensci.org/11a66ce121b349ecb26e7b35c06701789560449c9f2837ddf238c9c1871bb4b5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/36176068449"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.7.1",
      "date": "2026-09-25T18:58:25.000Z",
      "commit": "930823d38b94508b774cdd6bb33bfce82b9d4c79",
      "fileid": "https://r2.ropensci.org/5f2ad8136142666a2f249b5a879b7980a3e07bb4b0c932982bbf410e040a720b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/36176068449"
    }
  ]
}