{
  "_id": "6a3b62bd5cdecea1d681c90d",
  "Package": "PCSF",
  "Type": "Package",
  "Title": "Network-based interpretation of highthroughput data",
  "Version": "0.99.1",
  "Date": "2017-02-01",
  "Author": "Murodzhon Akhmedov, Amanda Kedaigle, Renan Escalante, Roberto\nMontemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee",
  "Maintainer": "Murodzhon Akhmedov <murodzhon@idsia.ch>",
  "Description": "The PCSF package performs an integrated analysis of\nhighthroughput data using the interaction networks as a\ntemplate, and interprets the biological landscape of\ninteraction networks with respect to the data, which\npotentially leads to predictions of functional units. It also\ninteractively visualize the resulting subnetwork with\nfunctional enrichment analysis.",
  "License": "MIT + file LICENSE",
  "RoxygenNote": "6.0.1",
  "Config/pak/sysreqs": "cmake libglpk-dev make libpng-dev libuv1-dev\nlibxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://cogdisreslab.r-universe.dev",
  "Date/Publication": "2019-05-07 09:02:15 UTC",
  "RemoteUrl": "https://github.com/CogDisResLab/PCSF",
  "RemoteRef": "HEAD",
  "RemoteSha": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-24 04:45:26 UTC",
    "User": "root"
  },
  "MD5sum": "c5c35ebe01820b9d03d12817aebecca1",
  "_user": "cogdisreslab",
  "_type": "src",
  "_file": "PCSF_0.99.1.tar.gz",
  "_fileid": "c05d7c049ff244fdc1915e9d485114fdfb6bd38d26b6babe6af518d5918febe0",
  "_filesize": 1838949,
  "_sha256": "c05d7c049ff244fdc1915e9d485114fdfb6bd38d26b6babe6af518d5918febe0",
  "_created": "2026-06-24T04:45:26.000Z",
  "_published": "2026-06-24T04:53:17.635Z",
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 83119654171,
      "time": 253,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7840392811"
    },
    {
      "job": 83119654156,
      "time": 283,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7840398062"
    },
    {
      "job": 83119654174,
      "time": 235,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7840389025"
    },
    {
      "job": 83119654161,
      "time": 251,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7840391916"
    },
    {
      "job": 83119654197,
      "time": 149,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7840369670"
    },
    {
      "job": 83119654196,
      "time": 335,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7840409700"
    },
    {
      "job": 83119654186,
      "time": 201,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7840380777"
    },
    {
      "job": 83119654258,
      "time": 420,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7840429274"
    },
    {
      "job": 83119217315,
      "time": 243,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7840337651"
    },
    {
      "job": 83119654113,
      "time": 220,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7840384753"
    },
    {
      "job": 83119654177,
      "time": 218,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7840384575"
    },
    {
      "job": 83119654205,
      "time": 227,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7840386603"
    },
    {
      "job": 83119654202,
      "time": 219,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7840384790"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28075632266",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/CogDisResLab/PCSF",
  "_commit": {
    "id": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78",
    "author": "murodzhon <murodzhon.akhmedov@irb.usi.ch>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update README.md",
    "time": 1557219735
  },
  "_maintainer": {
    "name": "Murodzhon Akhmedov",
    "email": "murodzhon@idsia.ch"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.1.0",
      "role": "Depends"
    },
    {
      "package": "igraph",
      "role": "Depends"
    },
    {
      "package": "visNetwork",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "BH",
      "role": "LinkingTo"
    },
    {
      "package": "BH",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "topGO",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cogdisreslab",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "murodzhon",
      "count": 51,
      "uuid": 20000070
    },
    {
      "user": "ivokwee",
      "count": 1,
      "uuid": 19613146
    }
  ],
  "_userbio": {
    "uuid": 83421213,
    "type": "organization",
    "name": "Cognitive Disorders Research Lab",
    "followers": 7
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PCSF"
  },
  "_devurl": "https://github.com/cogdisreslab/pcsf",
  "_searchresults": 93,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/PCSF.html",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "call_enr",
    "call_sr",
    "construct_interactome",
    "enrichment_analysis",
    "PCSF",
    "PCSF_rand",
    "plot.PCSF",
    "plot.PCSFe"
  ],
  "_datasets": [
    {
      "name": "STRING",
      "title": "Protein-protein interaction network data",
      "object": "STRING",
      "file": "STRING.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "from",
        "to",
        "cost"
      ],
      "rows": 175854,
      "table": true,
      "tojson": true
    },
    {
      "name": "Tgfb_phospho",
      "title": "Phosphoproteomic data",
      "object": "Tgfb_phospho",
      "file": "Tgfb_phospho.rda",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "construct_interactome",
      "title": "Construct an interaction network",
      "topics": [
        "construct_interactome"
      ]
    },
    {
      "page": "enrichment_analysis",
      "title": "Perform enrichment analysis on the subnetwork",
      "topics": [
        "enrichment_analysis"
      ]
    },
    {
      "page": "PCSF",
      "title": "Prize-collecting Steiner Forest (PCSF)",
      "topics": [
        "PCSF"
      ]
    },
    {
      "page": "PCSF_rand",
      "title": "Prize-collecting Steiner Forest (PCSF) with randomized edge costs",
      "topics": [
        "PCSF_rand"
      ]
    },
    {
      "page": "plot.PCSF",
      "title": "Plot an interactive subnetwork",
      "topics": [
        "plot.PCSF"
      ]
    },
    {
      "page": "plot.PCSFe",
      "title": "Plot an interactive subnetwork with functional enrichment analysis",
      "topics": [
        "plot.PCSFe"
      ]
    },
    {
      "page": "STRING",
      "title": "Protein-protein interaction network data",
      "topics": [
        "STRING"
      ]
    },
    {
      "page": "Tgfb_phospho",
      "title": "Phosphoproteomic data",
      "topics": [
        "Tgfb_phospho"
      ]
    }
  ],
  "_readme": "https://github.com/CogDisResLab/PCSF/raw/HEAD/README.md",
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "bslib",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "digest",
    "evaluate",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "glue",
    "GO.db",
    "graph",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "igraph",
    "IRanges",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "org.Hs.eg.db",
    "pkgconfig",
    "png",
    "R6",
    "rappdirs",
    "Rcpp",
    "rlang",
    "rmarkdown",
    "RSQLite",
    "S4Vectors",
    "sass",
    "Seqinfo",
    "SparseM",
    "sys",
    "tinytex",
    "topGO",
    "vctrs",
    "visNetwork",
    "xfun",
    "XVector",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 3.144574207609616,
  "_indexed": true,
  "_nocasepkg": "pcsf",
  "_universes": [
    "cogdisreslab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.1",
      "date": "2026-06-24T04:48:57.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78",
      "fileid": "d4be433bb9d9b124faa0ab1691d1b3c05dc0486b44f192c8a3f713c7fc880876",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28075632266"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.1",
      "date": "2026-06-24T04:49:09.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78",
      "fileid": "6fd6bc3b41930affe6ef70af6ec18006a8dbbb4118a01315026e35481c9b7660",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28075632266"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.99.1",
      "date": "2026-06-24T04:48:48.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78",
      "fileid": "8402dcdf8f102b4c82d9ce72bfd9522f98b83ef60fdd4f63990cb5f05a347922",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28075632266"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.99.1",
      "date": "2026-06-24T04:48:43.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78",
      "fileid": "52cc37a67b47f8af7535e35f1e01c851106409debf68c6be745c3c002f31d2d3",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28075632266"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.1",
      "date": "2026-06-24T04:47:30.000Z",
      "arch": "aarch64",
      "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78",
      "fileid": "398526c0b75f9528c98241d10a407330c46056c5fe5cd084559dfe8c831a3cd4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28075632266"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.1",
      "date": "2026-06-24T04:49:37.000Z",
      "arch": "x86_64",
      "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78",
      "fileid": "31512aa3348f2fadbf2e3d89b7d607de831a3766c4571e221218c1bd2240f22a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28075632266"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.99.1",
      "date": "2026-06-24T04:47:58.000Z",
      "arch": "aarch64",
      "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78",
      "fileid": "12ce215516a0449fad1915c128fcf237bbb1c20fb4cc33a9c91551256911d51c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28075632266"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.99.1",
      "date": "2026-06-24T04:50:36.000Z",
      "arch": "x86_64",
      "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78",
      "fileid": "40972f12e770477c6d957719cdfdde1f84889bd2efeada9d59fe04a69f3290df",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28075632266"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.1",
      "date": "2026-06-24T04:49:28.000Z",
      "arch": "emscripten",
      "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78",
      "fileid": "c4adc014d67ea18fa87efaaf03372de832416695711dd24ee8d5317db082bbc3",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28075632266"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.1",
      "date": "2026-06-24T04:47:47.000Z",
      "arch": "x86_64",
      "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78",
      "fileid": "f96fb2ce82892deb3e394e4dbfd4f234f469d51e3846111a38ae8d07a4ef667b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28075632266"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.1",
      "date": "2026-06-24T04:47:40.000Z",
      "arch": "x86_64",
      "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78",
      "fileid": "f16fd5b7da900bc02988791fdbfa8266e285db18b7512ee31c32c707e8e4c2fc",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28075632266"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.99.1",
      "date": "2026-06-24T04:47:43.000Z",
      "arch": "x86_64",
      "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78",
      "fileid": "1738603b70246cdec82cbae39eb64e20435c7a47970ea834e4cc5827218acedc",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/28075632266"
    }
  ]
}