{
  "_id": "6a49b2f2dbd0482285eb5872",
  "Package": "negenes",
  "Version": "1.4",
  "Date": "2025-12-08",
  "Title": "Estimating the Number of Essential Genes in a Genome",
  "Author": "Karl W Broman [aut, cre]\n(<https://orcid.org/0000-0002-4914-6671>)",
  "Maintainer": "Karl W Broman <broman@wisc.edu>",
  "Authors@R": "c(person(\"Karl W\", \"Broman\", role=c(\"aut\", \"cre\"),\nemail=\"broman@wisc.edu\", comment=c(ORCID = \"0000-0002-4914-6671\")))",
  "Description": "Estimating the number of essential genes in a genome on\nthe basis of data from a random transposon mutagenesis\nexperiment, through the use of a Gibbs sampler. Lamichhane et\nal. (2003) <doi:10.1073/pnas.1231432100>.",
  "License": "GPL (>= 3)",
  "URL": "https://github.com/kbroman/negenes",
  "BugReports": "https://github.com/kbroman/negenes/issues",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "Config/roxygen2/version": "8.0.0",
  "Repository": "https://kbroman.r-universe.dev",
  "Date/Publication": "2026-06-19 11:14:59 UTC",
  "RemoteUrl": "https://github.com/kbroman/negenes",
  "RemoteRef": "HEAD",
  "RemoteSha": "fed78ad40ab783358bb2e299ad90598bd0f3e6e8",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-19 13:37:42 UTC",
    "User": "root"
  },
  "_user": "kbroman",
  "_type": "src",
  "_file": "negenes_1.4.tar.gz",
  "_fileid": "https://r2.ropensci.org/6cacb8b13ab3933578921d151c46b8abe3d389d97f01c0c90fa4231d3e833aa6",
  "_filesize": 123176,
  "_sha256": "6cacb8b13ab3933578921d151c46b8abe3d389d97f01c0c90fa4231d3e833aa6",
  "_expires": "2026-10-13T01:27:12.000Z",
  "_created": "2026-06-19T13:37:42.000Z",
  "_published": "2026-07-05T01:27:14.425Z",
  "_jobs": [
    {
      "job": 85182453868,
      "time": 105,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7751145804"
    },
    {
      "job": 85182453853,
      "time": 109,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7751146363"
    },
    {
      "job": 85182454021,
      "time": 97,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7751143452"
    },
    {
      "job": 85182454000,
      "time": 102,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7751143846"
    },
    {
      "job": 85182454006,
      "time": 95,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7751165158"
    },
    {
      "job": 85182453916,
      "time": 160,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7751237470"
    },
    {
      "job": 85182453893,
      "time": 95,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7751161822"
    },
    {
      "job": 85182453825,
      "time": 209,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7751310085"
    },
    {
      "job": 85182453743,
      "time": 169,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7751106115"
    },
    {
      "job": 85182453917,
      "time": 87,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7751138501"
    },
    {
      "job": 85182453880,
      "time": 74,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7751134024"
    },
    {
      "job": 85182453908,
      "time": 60,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7751129415"
    },
    {
      "job": 85182453948,
      "time": 77,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7751135033"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/kbroman/actions/runs/27828914026",
  "_status": "success",
  "_upstream": "https://github.com/kbroman/negenes",
  "_commit": {
    "id": "fed78ad40ab783358bb2e299ad90598bd0f3e6e8",
    "author": "Karl Broman <kbroman@gmail.com>",
    "committer": "Karl Broman <kbroman@gmail.com>",
    "message": "Remove name from README\n",
    "time": 1781867699
  },
  "_maintainer": {
    "name": "Karl W Broman",
    "email": "broman@wisc.edu",
    "login": "kbroman",
    "mastodon": "@kbroman@rstats.me",
    "orcid": "0000-0002-4914-6671",
    "description": "Professor in Dept of Biostatistics & Medical Informatics at UW–Madison. Applied statistician working on statistical genomics.\n",
    "uuid": 53972
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10.1",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "roxygen2",
      "role": "Suggests"
    }
  ],
  "_owner": "kbroman",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-50",
      "n": 2
    },
    {
      "week": "2026-21",
      "n": 1
    },
    {
      "week": "2026-23",
      "n": 1
    },
    {
      "week": "2026-25",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "1.4",
      "date": "2025-12-08"
    }
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "kbroman",
      "count": 65,
      "uuid": 53972
    }
  ],
  "_userbio": {
    "uuid": 53972,
    "type": "user",
    "name": "Karl Broman",
    "followers": 1478,
    "description": "Professor in Dept of Biostatistics & Medical Informatics at UW–Madison. Applied statistician working on statistical genomics.\r\n"
  },
  "_downloads": {
    "count": 259,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/negenes"
  },
  "_devurl": "https://github.com/kbroman/negenes",
  "_searchresults": 5,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/negenes.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/kbroman/negenes",
  "_realowner": "kbroman",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.98-3",
      "date": "2003-06-20"
    },
    {
      "version": "0.98-4",
      "date": "2004-02-03"
    },
    {
      "version": "0.98-5",
      "date": "2004-06-30"
    },
    {
      "version": "0.98-6",
      "date": "2007-09-21"
    },
    {
      "version": "0.98-7",
      "date": "2007-10-09"
    },
    {
      "version": "0.98-8",
      "date": "2009-07-01"
    },
    {
      "version": "0.98-9",
      "date": "2011-03-21"
    },
    {
      "version": "0.99-2",
      "date": "2011-11-29"
    },
    {
      "version": "1.0-1",
      "date": "2012-04-09"
    },
    {
      "version": "1.0-3",
      "date": "2015-09-11"
    },
    {
      "version": "1.0-5",
      "date": "2016-05-22"
    },
    {
      "version": "1.0-8",
      "date": "2018-04-02"
    },
    {
      "version": "1.0-12",
      "date": "2019-08-05"
    },
    {
      "version": "1.2",
      "date": "2025-05-11"
    },
    {
      "version": "1.4",
      "date": "2025-12-11"
    }
  ],
  "_exports": [
    "negenes",
    "sim.mutants"
  ],
  "_datasets": [
    {
      "name": "Mtb80",
      "title": "Number of insertion sites in each gene in M tb CDC1551",
      "object": "Mtb80",
      "file": "Mtb80.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "n.sites",
        "n.sites2"
      ],
      "rows": 4204,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "Mtb80",
      "title": "Number of insertion sites in each gene in M tb CDC1551",
      "topics": [
        "Mtb80"
      ]
    },
    {
      "page": "negenes",
      "title": "Estimate the number of essential genes in a genome",
      "topics": [
        "negenes"
      ]
    },
    {
      "page": "sim.mutants",
      "title": "Simulate data for a random transposon mutagenesis experiment",
      "topics": [
        "sim.mutants"
      ]
    }
  ],
  "_readme": "https://github.com/kbroman/negenes/raw/HEAD/README.md",
  "_rundeps": [],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "negenes",
  "_universes": [
    "kbroman"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.4",
      "date": "2026-06-19T13:39:40.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "fed78ad40ab783358bb2e299ad90598bd0f3e6e8",
      "fileid": "https://r2.ropensci.org/09bb2f7026cf4a80412ff33e5f2fdfb3571012616ed67cef3a130ef507d2d5db",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kbroman/actions/runs/27828914026"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.4",
      "date": "2026-06-19T13:39:39.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "fed78ad40ab783358bb2e299ad90598bd0f3e6e8",
      "fileid": "https://r2.ropensci.org/be5105b5cfa648b63e0fdc3f0f865ba16e58c16c461c7185a1adfb0cea534d2b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kbroman/actions/runs/27828914026"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.4",
      "date": "2026-06-19T13:39:34.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "fed78ad40ab783358bb2e299ad90598bd0f3e6e8",
      "fileid": "https://r2.ropensci.org/41fc53cdf89213a177df83f0fe61776c4dbaf4baf5b91d04406ab6823e3b0fe5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kbroman/actions/runs/27828914026"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.4",
      "date": "2026-06-19T13:39:33.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "fed78ad40ab783358bb2e299ad90598bd0f3e6e8",
      "fileid": "https://r2.ropensci.org/60d536a903b369156ad082d9a7ce2b0d81472e2ee163623767700b6db7d3f5e5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kbroman/actions/runs/27828914026"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.4",
      "date": "2026-06-19T13:40:26.000Z",
      "arch": "aarch64",
      "commit": "fed78ad40ab783358bb2e299ad90598bd0f3e6e8",
      "fileid": "https://r2.ropensci.org/3254ad7162aee020b77d16dc52c2ae9fcc070c1a5c0cbceaa0756bf2bb8f9f6a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kbroman/actions/runs/27828914026"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.4",
      "date": "2026-06-19T13:43:54.000Z",
      "arch": "x86_64",
      "commit": "fed78ad40ab783358bb2e299ad90598bd0f3e6e8",
      "fileid": "https://r2.ropensci.org/e6611acd8dcfdbe23a829a3ef4042020f2a6a4a68afcbfd2efb01929a4b99246",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kbroman/actions/runs/27828914026"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.4",
      "date": "2026-06-19T13:40:19.000Z",
      "arch": "aarch64",
      "commit": "fed78ad40ab783358bb2e299ad90598bd0f3e6e8",
      "fileid": "https://r2.ropensci.org/6a3342d8ae752da7a7636e8d1d5fcdbd34195784f172321613cfca03db18dc26",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kbroman/actions/runs/27828914026"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.4",
      "date": "2026-06-19T13:47:05.000Z",
      "arch": "x86_64",
      "commit": "fed78ad40ab783358bb2e299ad90598bd0f3e6e8",
      "fileid": "https://r2.ropensci.org/8a8e160439a20ef2ae6f09ec7cfa5c7b259befcf3fc00e8cc66eb33a91c1e272",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kbroman/actions/runs/27828914026"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.4",
      "date": "2026-06-19T13:39:26.000Z",
      "arch": "emscripten",
      "commit": "fed78ad40ab783358bb2e299ad90598bd0f3e6e8",
      "fileid": "https://r2.ropensci.org/f9f7129c11b473ea95866c733ed58c235070a595a34fb60e885e4de79ad1a681",
      "status": "success",
      "buildurl": "https://github.com/r-universe/kbroman/actions/runs/27828914026"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.4",
      "date": "2026-06-19T13:38:52.000Z",
      "arch": "x86_64",
      "commit": "fed78ad40ab783358bb2e299ad90598bd0f3e6e8",
      "fileid": "https://r2.ropensci.org/0090c593c2bb4144adeb90109b6f519d68eccec30ad91fc892ba5c62aed08df8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kbroman/actions/runs/27828914026"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.4",
      "date": "2026-06-19T13:38:44.000Z",
      "arch": "x86_64",
      "commit": "fed78ad40ab783358bb2e299ad90598bd0f3e6e8",
      "fileid": "https://r2.ropensci.org/2a41862f5231b4c006ed8a36248caba4947ea4f57ac39395e440ba3a9367a115",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kbroman/actions/runs/27828914026"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.4",
      "date": "2026-06-19T13:38:59.000Z",
      "arch": "x86_64",
      "commit": "fed78ad40ab783358bb2e299ad90598bd0f3e6e8",
      "fileid": "https://r2.ropensci.org/d0fcec7bdd873ce78e6feb65b1b37af3537c7e3fe8cbe580b831ae44010dd336",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kbroman/actions/runs/27828914026"
    }
  ]
}