{
  "_id": "6acf53cbd9de2f3f33fcb0f0",
  "Package": "netcutter",
  "Type": "Package",
  "Title": "Identification and Analysis of Co-Occurrence Networks",
  "Version": "0.3.1",
  "Authors@R": "c(\nperson(\"Heiko\", \"Müller\", role = \"aut\"),\nperson(\"Francesco\", \"Mancuso\", role = \"aut\"),\nperson(\"Federico\", \"Marotta\", email = \"federico.marotta@embl.de\", role = \"cre\"))",
  "Maintainer": "Federico Marotta <federico.marotta@embl.de>",
  "Description": "Implementation of the NetCutter algorithm described in\nMüller and Mancuso (2008) <doi:10.1371/journal.pone.0003178>.\nThe package identifies co-occurring terms in a list of\ncontainers. For example, it may be used to detect genes that\nco-occur across genomes.",
  "URL": "https://doi.org/10.1371/journal.pone.0003178",
  "BugReports": "https://github.com/fmarotta/netcutter/issues",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Config/testthat/edition": "3",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libfftw3-dev",
  "Repository": "https://fmarotta.r-universe.dev",
  "Date/Publication": "2025-05-30 11:39:34 UTC",
  "RemoteUrl": "https://github.com/fmarotta/netcutter",
  "RemoteRef": "HEAD",
  "RemoteSha": "1a2027310a9e093d8c982b0a5d8f4014850434a7",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-14 09:39:55 UTC",
    "User": "root"
  },
  "Author": "Heiko Müller [aut],\nFrancesco Mancuso [aut],\nFederico Marotta [cre]",
  "_user": "fmarotta",
  "_type": "src",
  "_file": "netcutter_0.3.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/b16077d4fcfc2b6efdde7742a191efe9630f30648c46285779b94c66187bdca6",
  "_filesize": 115742,
  "_sha256": "b16077d4fcfc2b6efdde7742a191efe9630f30648c46285779b94c66187bdca6",
  "_expires": "2027-01-22T10:04:57.000Z",
  "_created": "2026-10-14T09:39:55.000Z",
  "_published": "2026-10-14T10:04:58.928Z",
  "_buildurl": "https://github.com/r-universe/fmarotta/actions/runs/38543610707",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 115785611275,
      "time": 168,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11882954572"
    },
    {
      "job": 115785611114,
      "time": 137,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11883916592"
    },
    {
      "job": 115785611115,
      "time": 112,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11884154730"
    },
    {
      "job": 115785611368,
      "time": 99,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11884279987"
    },
    {
      "job": 115784271258,
      "time": 195,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11883078786"
    },
    {
      "job": 115785611145,
      "time": 97,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11883338268"
    },
    {
      "job": 115785612068,
      "time": 75,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11884051250"
    },
    {
      "job": 115785611201,
      "time": 78,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11883039032"
    },
    {
      "job": 115785611365,
      "time": 67,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11883971285"
    }
  ],
  "_upstream": "https://github.com/fmarotta/netcutter",
  "_commit": {
    "id": "1a2027310a9e093d8c982b0a5d8f4014850434a7",
    "author": "Federico Marotta <fmarotta@protonmail.com>",
    "committer": "Federico Marotta <fmarotta@protonmail.com>",
    "message": "update badges\n",
    "time": 1748605174
  },
  "_maintainer": {
    "name": "Federico Marotta",
    "email": "federico.marotta@embl.de",
    "login": "fmarotta",
    "twitter": "@fede_maro",
    "description": ":wq",
    "uuid": 26001460
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "PoissonBinomial",
      "role": "Imports"
    },
    {
      "package": "rlecuyer",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "qpdf",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "fmarotta",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "fmarotta",
      "count": 35,
      "uuid": 26001460
    }
  ],
  "_userbio": {
    "uuid": 26001460,
    "type": "user",
    "name": "Federico Marotta",
    "followers": 67,
    "description": ":wq"
  },
  "_downloads": {
    "count": 304,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/netcutter"
  },
  "_devurl": "https://github.com/fmarotta/netcutter",
  "_searchresults": 4,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/netcutter.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/fmarotta/netcutter",
  "_realowner": "fmarotta",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.3.1",
      "date": "2025-05-21"
    }
  ],
  "_exports": [
    "nc_eval",
    "nc_occ_probs"
  ],
  "_help": [
    {
      "page": "nc_define_modules",
      "title": "Define co-occurrence modules",
      "topics": [
        "nc_define_modules"
      ]
    },
    {
      "page": "nc_eval",
      "title": "Compute co-occurrence probabilities",
      "topics": [
        "nc_eval"
      ]
    },
    {
      "page": "nc_occ_probs",
      "title": "Compute the occurrence probabilities",
      "topics": [
        "nc_occ_probs"
      ]
    },
    {
      "page": "nc_occ_probs_simple",
      "title": "Compute the occurrence probabilities",
      "topics": [
        "nc_occ_probs_simple"
      ]
    },
    {
      "page": "nc_randomize",
      "title": "Randomize the occurrence matrix",
      "topics": [
        "nc_randomize"
      ]
    },
    {
      "page": "nc_randomize_fast",
      "title": "Randomize the occurrence matrix",
      "topics": [
        "nc_randomize_fast"
      ]
    },
    {
      "page": "nc_randomize_R",
      "title": "Randomize the occurrence matrix",
      "topics": [
        "nc_randomize_R"
      ]
    },
    {
      "page": "nc_randomize_simple",
      "title": "Randomize the occurrence matrix",
      "topics": [
        "nc_randomize_simple"
      ]
    },
    {
      "page": "safe_sample",
      "title": "Sample one item from a vector, even when the vector has length 1",
      "topics": [
        "safe_sample"
      ]
    }
  ],
  "_readme": "https://github.com/fmarotta/netcutter/raw/HEAD/README.md",
  "_rundeps": [
    "PoissonBinomial",
    "Rcpp",
    "rlecuyer"
  ],
  "_vignettes": [
    {
      "source": "netcutter.Rmd",
      "filename": "netcutter.html",
      "title": "netcutter",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "NOTE",
        "Usage",
        "Data preparation",
        "nc_occ_probs()",
        "nc_eval()"
      ],
      "created": "2023-07-31 18:30:02",
      "modified": "2025-05-19 19:57:17",
      "commits": 9
    }
  ],
  "_score": 3.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "netcutter",
  "_universes": [
    "fmarotta"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.3.1",
      "date": "2026-10-14T09:42:43.000Z",
      "distro": "resolute",
      "commit": "1a2027310a9e093d8c982b0a5d8f4014850434a7",
      "fileid": "https://r2.ropensci.org/58d06ff9a8fa568378b828432e432ac4209804b90b2ee828ae3ade0b4f8b5b9b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fmarotta/actions/runs/38543610707"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.3.1",
      "date": "2026-10-14T09:42:14.000Z",
      "distro": "resolute",
      "commit": "1a2027310a9e093d8c982b0a5d8f4014850434a7",
      "fileid": "https://r2.ropensci.org/ec6dd4225d1ebe3c7f742114271fd5c9d8ed08674ecf35c5287f346a5c943a10",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fmarotta/actions/runs/38543610707"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.3.1",
      "date": "2026-10-14T10:01:25.000Z",
      "commit": "1a2027310a9e093d8c982b0a5d8f4014850434a7",
      "fileid": "https://r2.ropensci.org/b076902324e8508cb238688e23f918bd6aa1bbc7320d3ba395c9ab9b178a6451",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fmarotta/actions/runs/38543610707"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.3.1",
      "date": "2026-10-14T10:04:24.000Z",
      "commit": "1a2027310a9e093d8c982b0a5d8f4014850434a7",
      "fileid": "https://r2.ropensci.org/95e15798cb2929c09ee73f6577f85e905a07dcbdef2dede667412eeae8320470",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fmarotta/actions/runs/38543610707"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.3.1",
      "date": "2026-10-14T09:41:54.000Z",
      "commit": "1a2027310a9e093d8c982b0a5d8f4014850434a7",
      "fileid": "https://r2.ropensci.org/f8784524c588cfa94445d0e1b85c42fd0862cf9b85740fdefa1d00a0d5d066d7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/fmarotta/actions/runs/38543610707"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.3.1",
      "date": "2026-10-14T09:41:11.000Z",
      "commit": "1a2027310a9e093d8c982b0a5d8f4014850434a7",
      "fileid": "https://r2.ropensci.org/5f1e2955cbc17ee0087622a523011fa1589a5cc394e51f076f1ce78be9f5f327",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fmarotta/actions/runs/38543610707"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.3.1",
      "date": "2026-10-14T09:41:10.000Z",
      "commit": "1a2027310a9e093d8c982b0a5d8f4014850434a7",
      "fileid": "https://r2.ropensci.org/26e62c8308d59297ece7c3a95026e94a754e5d47fae223bcc3932a34067f9571",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fmarotta/actions/runs/38543610707"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.3.1",
      "date": "2026-10-14T09:41:05.000Z",
      "commit": "1a2027310a9e093d8c982b0a5d8f4014850434a7",
      "fileid": "https://r2.ropensci.org/bcc4ca31e48a3ce76b7a987dc6694138c6ad53242fac5c8f8c20ab37ed01d68d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fmarotta/actions/runs/38543610707"
    }
  ]
}