{
  "_id": "6a5f1b1014e95619b75d3faf",
  "Package": "bc3net",
  "Version": "1.0.5",
  "Date": "2025-05-06",
  "Title": "Gene Regulatory Network Inference with Bc3net",
  "Authors@R": "c(person(\"Ricardo\", \"de Matos Simoes\", role=c(\"aut\",\"cre\"),\nemail=\"ricardo_dematossimoes@dfci.harvard.edu\"),\nperson(\"Frank\", \"Emmert-Streib\", role=c(\"aut\"),\nemail=\"v@bio-complexity.com\"))",
  "Author": "Ricardo de Matos Simoes [aut, cre], Frank Emmert-Streib [aut]",
  "Maintainer": "Ricardo de Matos Simoes\n<ricardo_dematossimoes@dfci.harvard.edu>",
  "Description": "Implementation of the BC3NET algorithm for gene regulatory\nnetwork inference (de Matos Simoes and Frank Emmert-Streib,\nBagging Statistical Network Inference from Large-Scale Gene\nExpression Data, PLoS ONE 7(3): e33624,\n<doi:10.1371/journal.pone.0033624>).",
  "License": "GPL (>= 2)",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-21 07:05:33 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://bio-complexity.r-universe.dev",
  "Date/Publication": "2025-05-06 20:36:14 UTC",
  "RemoteUrl": "https://github.com/cran/bc3net",
  "RemoteRef": "HEAD",
  "RemoteSha": "1236792160b0a61c885faf998b6c25d99ba3ce16",
  "_user": "bio-complexity",
  "_type": "src",
  "_file": "bc3net_1.0.5.tar.gz",
  "_fileid": "https://r2.ropensci.org/b08c372047ff31d0a3ab18e1b4864322e802928a860851410b051852d037a160",
  "_filesize": 217691,
  "_sha256": "b08c372047ff31d0a3ab18e1b4864322e802928a860851410b051852d037a160",
  "_expires": "2026-10-29T07:09:02.000Z",
  "_created": "2026-07-21T07:05:33.000Z",
  "_published": "2026-07-21T07:09:04.054Z",
  "_jobs": [
    {
      "job": 88566252335,
      "time": 133,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8486755254"
    },
    {
      "job": 88566252436,
      "time": 150,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8486762079"
    },
    {
      "job": 88566252368,
      "time": 170,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8486759602"
    },
    {
      "job": 88566252407,
      "time": 148,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8486752376"
    },
    {
      "job": 88565744602,
      "time": 160,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8486700065"
    },
    {
      "job": 88566252369,
      "time": 100,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8486741706"
    },
    {
      "job": 88566252373,
      "time": 88,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8486738473"
    },
    {
      "job": 88566252445,
      "time": 80,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8486734369"
    },
    {
      "job": 88566252364,
      "time": 107,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8486744788"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bio-complexity/actions/runs/29809006315",
  "_status": "success",
  "_upstream": "https://github.com/cran/bc3net",
  "_commit": {
    "id": "1236792160b0a61c885faf998b6c25d99ba3ce16",
    "author": "Ricardo de Matos Simoes <ricardo_dematossimoes@dfci.harvard.edu>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0.5\n",
    "time": 1746563774
  },
  "_maintainer": {
    "name": "Ricardo de Matos Simoes",
    "email": "ricardo_dematossimoes@dfci.harvard.edu",
    "login": "bio-complexity",
    "description": "",
    "uuid": 23239081
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "c3net",
      "role": "Depends"
    },
    {
      "package": "infotheo",
      "role": "Depends"
    },
    {
      "package": "igraph",
      "role": "Depends"
    },
    {
      "package": "Matrix",
      "role": "Depends"
    },
    {
      "package": "lattice",
      "role": "Depends"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "bio-complexity",
      "count": 3,
      "uuid": 23239081
    }
  ],
  "_userbio": {
    "uuid": 23239081,
    "type": "user",
    "name": "rdms",
    "followers": 0
  },
  "_downloads": {
    "count": 445,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bc3net"
  },
  "_mentions": 2,
  "_searchresults": 87,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/bc3net.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "manual.pdf"
  ],
  "_realowner": "bio-complexity",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2012-08-29"
    },
    {
      "version": "1.0.1",
      "date": "2013-02-27"
    },
    {
      "version": "1.0.2",
      "date": "2013-04-07"
    },
    {
      "version": "1.0.3",
      "date": "2015-12-30"
    },
    {
      "version": "1.0.4",
      "date": "2016-11-28"
    },
    {
      "version": "1.0.5",
      "date": "2025-05-06"
    }
  ],
  "_exports": [
    "bc3net",
    "c3mtc",
    "enrichment",
    "getgcc",
    "gpea",
    "makenull",
    "mimwrap"
  ],
  "_datasets": [
    {
      "name": "exanet",
      "title": "Example gene regulatory network for testing purposes only",
      "object": "exanet",
      "file": "exanet.rda",
      "class": [
        "igraph"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "exgensets",
      "title": "Example gene sets defined from the CPDB database",
      "object": "exgensets",
      "file": "exgensets.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "expmat",
      "title": "Test gene expression dataset",
      "object": "expmat",
      "file": "expmat.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "SD8_sporulation_DMSO_4hr_r1",
        "SD8_sporulation_DMSO_4hr_r1.1",
        "SD5_sporulation_DMSO_1hr_r1",
        "SD5_sporulation_DMSO_1hr_r1.1",
        "SB8_sporulation_benomyl_4hr_r1",
        "SB8_sporulation_benomyl_4hr_r1.1",
        "SB5_sporulation_benomyl_1hr_r1",
        "SB5_sporulation_benomyl_1hr_r1.1",
        "SF5_sporulation_initial_4hr_plus_1hr_r1",
        "SF5_sporulation_initial_4hr_plus_1hr_r1.1",
        "SP4_sporulation_initial_4hr_r1",
        "SP4_sporulation_initial_4hr_r1.1",
        "YPA_pre_sporulation_control_r1",
        "YPA_pre_sporulation_control_r1.1",
        "YPD_general_control_r1",
        "YPD_general_control_r1.1",
        "SC5_sporulation_cold_1hr_r1",
        "SC5_sporulation_cold_1hr_r1.1",
        "SC8_sporulation_cold_4hr_r1",
        "SC8_sporulation_cold_4hr_r1.1",
        "SR4_sporulation_initial_4hr_control_for.SC_expt_r1",
        "SR4_sporulation_initial_4hr_control_for.SC_expt_r1.1",
        "SR5_sporulation_initial_4hr_plus_1hr_control_for_SC5_r1",
        "SR5_sporulation_initial_4hr_plus_1hr_control_for_SC5_r1.1",
        "SR8_sporulation_control_for_SC8_r1",
        "SR8_sporulation_control_for_SC8_r1.1",
        "wildtype.YSS37._T0_r1",
        "wildtype.YSS37._T30_r1",
        "wildtype.YSS37._T60_r1",
        "wildtype.YSS37._T0_r1.1",
        "wildtype.YSS37._T30_r1.1",
        "wildtype.YSS37._T60_r1.1",
        "wildtype.YSS37._T0_r1.2",
        "wildtype.YSS37._T30_r1.2",
        "wildtype.YSS37._T60_r1.2",
        "IFH1induced.YSS89._T0_r1",
        "IFH1induced.YSS89._T20_r1",
        "IFH1induced.YSS89._T30_r1",
        "IFH1induced.YSS89._T40_r1",
        "IFH1induced.YSS89._T60_r1",
        "IFH1induced.YSS89._T0_r1.1",
        "IFH1induced.YSS89._T20_r1.1",
        "IFH1induced.YSS89._T30_r1.1",
        "IFH1induced.YSS89._T40_r1.1",
        "IFH1induced.YSS89._T60_r1.1",
        "IFH1induced.YSS89._T0_r1.2",
        "IFH1induced.YSS89._T20_r1.2",
        "IFH1induced.YSS89._T30_r1.2",
        "IFH1induced.YSS89._T40_r1.2",
        "IFH1induced.YSS89._T60_r1.2",
        "del_gpa2_r1",
        "del_gpa2_r1.1",
        "del_gpr1_r1",
        "del_gpr1_r1.1",
        "wt_W303.1A_r1",
        "wt_W303.1A_r1.1",
        "del_PMI40_0pt75_g_per_L_initial_mannose_r1",
        "del_PMI40_0pt75_g_per_L_initial_mannose_r1.1",
        "del_PMI40_0pt75_g_per_L_initial_mannose_r1.2",
        "del_PMI40_3_g_per_L_initial_mannose_r1",
        "del_PMI40_3_g_per_L_initial_mannose_r1.1",
        "del_PMI40_3_g_per_L_initial_mannose_r1.2",
        "del_PMI40_5_g_per_L_initial_mannose_r1",
        "del_PMI40_5_g_per_L_initial_mannose_r1.1",
        "del_PMI40_5_g_per_L_initial_mannose_r1.2",
        "del_PMI40_1pt5_g_per_L_initial_mannose_r1",
        "del_PMI40_1pt5_g_per_L_initial_mannose_r1.1",
        "del_PMI40_1pt5_g_per_L_initial_mannose_r1.2",
        "del_PMI40_1_g_per_L_initial_mannose_r1",
        "del_PMI40_1_g_per_L_initial_mannose_r1.1",
        "del_PMI40_1_g_per_L_initial_mannose_r1.2",
        "BY_haploid_r1",
        "BY_haploid_r1.1",
        "BY_haploid_r1.2",
        "RM_haploid_r1",
        "RM_haploid_r1.1",
        "RM_haploid_r1.2",
        "BYxRM_diploid_r1",
        "BYxRM_diploid_r1.1",
        "BYxRM_diploid_r1.2",
        "BYxRM_diploid_r1.3",
        "BYxRM_diploid_r1.4",
        "BYxRM_diploid_r1.5",
        "Segregant_r1",
        "Segregant_r1.1",
        "BY_diploid_r1",
        "BY_diploid_r1.1",
        "BY_diploid_r1.2",
        "RM_diploid_r1",
        "RM_diploid_r1.1",
        "RM_diploid_r1.2",
        "Segregant_diploid._hybrid_r1",
        "Segregant_diploid._hybrid_r1.1",
        "WT_histoneH3H4_rpd3_study_r1",
        "WT_histoneH3H4_rpd3_study_r1.1",
        "WT_histoneH3H4_rpd3_study_r1.2",
        "del_rpd3_r1",
        "del_rpd3_r1.1",
        "H3del.1.28._r1",
        "H3del.1.28._r1.1"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "bc3net-package",
      "title": "BC3NET Gene Regulatory network Inference",
      "topics": [
        "bc3net-package"
      ]
    },
    {
      "page": "bc3net",
      "title": "Bc3net gene regulatory network inference",
      "topics": [
        "bc3net"
      ]
    },
    {
      "page": "c3mtc",
      "title": "'c3mtc' gene regulatory network inference using c3net with multiple testing correction procedure",
      "topics": [
        "c3mtc"
      ]
    },
    {
      "page": "enrichment",
      "title": "Function that performs a functional enrichment analysis based on a one-sided Fisher's exact teset (hypergeometric test).",
      "topics": [
        "enrichment"
      ]
    },
    {
      "page": "exanet",
      "title": "Example gene regulatory network for testing purposes only",
      "topics": [
        "exanet"
      ]
    },
    {
      "page": "exgensets",
      "title": "Example gene sets defined from the CPDB database",
      "topics": [
        "exgensets"
      ]
    },
    {
      "page": "expmat",
      "title": "Test gene expression dataset",
      "topics": [
        "expmat"
      ]
    },
    {
      "page": "getgcc",
      "title": "Extracting the giant connected component from an igraph object",
      "topics": [
        "getgcc"
      ]
    },
    {
      "page": "gpea",
      "title": "Gene pair enrichment analysis (GPEA)",
      "topics": [
        "gpea"
      ]
    },
    {
      "page": "mimwrap",
      "title": "Wrapper function for mutual information matrix estimators",
      "topics": [
        "mimwrap"
      ]
    }
  ],
  "_rundeps": [
    "c3net",
    "cli",
    "cpp11",
    "glue",
    "igraph",
    "infotheo",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "pkgconfig",
    "rlang",
    "vctrs"
  ],
  "_score": 2.2405492482825995,
  "_indexed": true,
  "_nocasepkg": "bc3net",
  "_universes": [
    "bio-complexity"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.5",
      "date": "2026-07-21T07:07:30.000Z",
      "distro": "resolute",
      "commit": "1236792160b0a61c885faf998b6c25d99ba3ce16",
      "fileid": "https://r2.ropensci.org/cd89bfe67d08e2e712a61edab9e2f7fd6a73ea64b8dbe088ea41b0a217acc3f6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bio-complexity/actions/runs/29809006315"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.5",
      "date": "2026-07-21T07:07:52.000Z",
      "distro": "resolute",
      "commit": "1236792160b0a61c885faf998b6c25d99ba3ce16",
      "fileid": "https://r2.ropensci.org/8dc9edbb25db36ab0cf4915fc99c5c1883d07d1d0df35526dee016df37a43b18",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bio-complexity/actions/runs/29809006315"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.5",
      "date": "2026-07-21T07:07:50.000Z",
      "commit": "1236792160b0a61c885faf998b6c25d99ba3ce16",
      "fileid": "https://r2.ropensci.org/5c5baca07242dd7fa31fda407439a5a25ee719115bfa2d14d422201e77e6898a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bio-complexity/actions/runs/29809006315"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.5",
      "date": "2026-07-21T07:07:33.000Z",
      "commit": "1236792160b0a61c885faf998b6c25d99ba3ce16",
      "fileid": "https://r2.ropensci.org/995136583c9f69b5973b8dc6227d56c08e1497e1d4834015e52476a8623c91c5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bio-complexity/actions/runs/29809006315"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.5",
      "date": "2026-07-21T07:07:27.000Z",
      "commit": "1236792160b0a61c885faf998b6c25d99ba3ce16",
      "fileid": "https://r2.ropensci.org/ceed6ffae46e24fcac1acca949033a1ab364b9867ecf38b9059a984c1796f92d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bio-complexity/actions/runs/29809006315"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.5",
      "date": "2026-07-21T07:06:48.000Z",
      "commit": "1236792160b0a61c885faf998b6c25d99ba3ce16",
      "fileid": "https://r2.ropensci.org/b08bdbc139eb54b7c5f491438669328e9770d1aefa747a9da04676bb8119d2fa",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bio-complexity/actions/runs/29809006315"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.5",
      "date": "2026-07-21T07:06:37.000Z",
      "commit": "1236792160b0a61c885faf998b6c25d99ba3ce16",
      "fileid": "https://r2.ropensci.org/ed69cbbff06febd6be5991b43b871ebe3ebdaf831b9894eb5eca9f6034cf0d7a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bio-complexity/actions/runs/29809006315"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.5",
      "date": "2026-07-21T07:07:00.000Z",
      "commit": "1236792160b0a61c885faf998b6c25d99ba3ce16",
      "fileid": "https://r2.ropensci.org/7c7f83d26cf0db2e7689ce5a8477e87df0b14839f548a038184ee3644632e061",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bio-complexity/actions/runs/29809006315"
    }
  ]
}