{
  "_id": "69eaf434c5259ad4cda58dec",
  "Package": "BAGS",
  "Type": "Package",
  "Title": "A Bayesian Approach for Geneset Selection",
  "Version": "2.51.0",
  "Date": "2013-06-12",
  "Author": "Alejandro Quiroz-Zarate",
  "Maintainer": "Alejandro Quiroz-Zarate <aquiroz@jimmy.harvard.edu>",
  "Description": "R package providing functions to perform geneset\nsignificance analysis over simple cross-sectional data between\n2 and 5 phenotypes of interest.",
  "License": "Artistic-2.0",
  "Collate": "DataGeneSets.R Gibbs5.R Gibbs4.R Gibbs3.R Gibbs2.R GrpMean.R\nMCMCDataSet.R ReadGMT.R",
  "LazyLoad": "yes",
  "URL http": "//compbio.dfci.harvard.edu/",
  "biocViews": "Bayesian",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2025-10-29 14:10:06 UTC",
  "RemoteUrl": "https://github.com/bioc/BAGS",
  "RemoteRef": "HEAD",
  "RemoteSha": "7085f8116810f29f596111a333281b4fe92eb431",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-04-22 09:04:18 UTC",
    "User": "root"
  },
  "MD5sum": "4bf62fd8209b931f1838d73b1118c947",
  "_user": "bioc",
  "_type": "src",
  "_file": "BAGS_2.51.0.tar.gz",
  "_fileid": "de877fb57a9d49b37d1d14698479818be45e28d6bd5f106565bacbdfebc3007a",
  "_filesize": 328537,
  "_sha256": "de877fb57a9d49b37d1d14698479818be45e28d6bd5f106565bacbdfebc3007a",
  "_created": "2026-04-22T09:04:18.000Z",
  "_jobs": [
    {
      "job": 72821644585,
      "time": 139,
      "config": "bioc-checks",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "6617290456"
    },
    {
      "job": 72821644715,
      "time": 93,
      "config": "linux-devel-arm64",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 72821644720,
      "time": 144,
      "config": "linux-devel-x86_64",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 72821644939,
      "time": 126,
      "config": "linux-release-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6574405359"
    },
    {
      "job": 72821644811,
      "time": 181,
      "config": "linux-release-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6574422104"
    },
    {
      "job": 72821644946,
      "time": 125,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6575213562"
    },
    {
      "job": 72821644887,
      "time": 328,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6574475547"
    },
    {
      "job": 72821644710,
      "time": 80,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 72821644727,
      "time": 191,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 72821644755,
      "time": 133,
      "config": "source",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6574367372"
    },
    {
      "job": 72821644812,
      "time": 92,
      "config": "wasm-release",
      "r": "4.5.1",
      "check": "OK",
      "artifact": "6574395333"
    },
    {
      "job": 72821644672,
      "time": 53,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 72821644929,
      "time": 91,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6574395108"
    },
    {
      "job": 72821644675,
      "time": 65,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 2,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/24769770699",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/BAGS",
  "_commit": {
    "id": "7085f8116810f29f596111a333281b4fe92eb431",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_22 branch\n",
    "time": 1761747006
  },
  "_maintainer": {
    "name": "Alejandro Quiroz-Zarate",
    "email": "aquiroz@jimmy.harvard.edu"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "breastCancerVDX",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.51.0",
      "bioc": "3.23"
    },
    {
      "branch": "release",
      "version": "2.50.0",
      "bioc": "3.22"
    }
  ],
  "_topics": [
    "bayesian"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 444,
    "source": "https://www.bioconductor.org/packages/stats/bioc/BAGS"
  },
  "_mentions": 3,
  "_searchresults": 47,
  "_rbuild": "4.5.3",
  "_assets": [
    "extra/BAGS.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "DataGeneSets",
    "Gibbs2",
    "Gibbs3",
    "Gibbs4",
    "Gibbs5",
    "MCMCDataSet",
    "ReadGMT"
  ],
  "_datasets": [
    {
      "name": "AnnotationMFGO",
      "title": "List containing a collection of gene symbols with their associated GO term for the Molecular function ontology",
      "object": "AnnotationMFGO",
      "file": "AnnotationMFGO.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "BAGS-package",
      "title": "A Bayesian Approach for Geneset Selection (BAGS).",
      "topics": [
        "BAGS-package",
        "BAGS"
      ]
    },
    {
      "page": "AnnotationMFGO",
      "title": "List containing a collection of gene symbols with their associated GO term for the Molecular function ontology",
      "topics": [
        "AnnotationMFGO"
      ]
    },
    {
      "page": "DataGeneSets",
      "title": "Function that filters the gene sets to work with the desired size.",
      "topics": [
        "DataGeneSets"
      ]
    },
    {
      "page": "Gibbs2",
      "title": "Function obtains the MCMC chains for the parameters of interest that will form their posterior distribution.",
      "topics": [
        "Gibbs2"
      ]
    },
    {
      "page": "Gibbs3",
      "title": "Function obtains the MCMC chains for the parameters of interest that will form their posterior distribution.",
      "topics": [
        "Gibbs3"
      ]
    },
    {
      "page": "Gibbs4",
      "title": "Function obtains the MCMC chains for the parameters of interest that will form their posterior distribution.",
      "topics": [
        "Gibbs4"
      ]
    },
    {
      "page": "Gibbs5",
      "title": "Function obtains the MCMC chains for the parameters of interest that will form their posterior distribution.",
      "topics": [
        "Gibbs5"
      ]
    },
    {
      "page": "MCMCDataSet",
      "title": "Function that transform the dataset into the required format for the Gibbs sampler.",
      "topics": [
        "MCMCDataSet"
      ]
    },
    {
      "page": "ReadGMT",
      "title": "Function that extracts the gene set definition from a .gmt file.",
      "topics": [
        "ReadGMT"
      ]
    }
  ],
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "breastCancerVDX",
    "generics"
  ],
  "_vignettes": [
    {
      "source": "BAGS.Rnw",
      "filename": "BAGS.pdf",
      "title": "BAGS: A Bayesian Approach for Geneset Selection.",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 20:23:23",
      "modified": "2018-09-06 18:31:39",
      "commits": 3
    }
  ],
  "_score": 4.14921911265538,
  "_indexed": true,
  "_nocasepkg": "bags",
  "_universes": [
    "bioc"
  ],
  "_failure": {
    "version": "2.53.0",
    "commit": {
      "id": "dcd0b6e846a16b0e13cf631ccdf564d0f36df8c5",
      "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
      "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
      "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
      "time": 1777379772
    },
    "buildurl": "https://github.com/r-universe/bioc/actions/runs/26847356675",
    "date": "2026-06-05T06:01:52.397Z",
    "job": {
      "job": 79672733690,
      "time": 127,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7429871189"
    }
  },
  "_binaries": [
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.51.0",
      "date": "2026-04-22T09:50:29.000Z",
      "arch": "aarch64",
      "commit": "7085f8116810f29f596111a333281b4fe92eb431",
      "fileid": "9046f190e7db55e29718cb48f913da7f12f6895ce231d9f04f1ad12b7ce14f19",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/24769770699"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.51.0",
      "date": "2026-04-22T09:09:09.000Z",
      "arch": "x86_64",
      "commit": "7085f8116810f29f596111a333281b4fe92eb431",
      "fileid": "1b5131e3a6013eca3849416d0264b6d10f52e2a155f032de160065e9d063f176",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/24769770699"
    },
    {
      "r": "4.5.1",
      "os": "wasm",
      "version": "2.51.0",
      "date": "2026-04-22T09:06:05.000Z",
      "arch": "emscripten",
      "commit": "7085f8116810f29f596111a333281b4fe92eb431",
      "fileid": "6ef177d85b849765081a50c0f256cf50904cbc38c62709e9dbc66cd2e33afc20",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/24769770699"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.51.0",
      "date": "2026-04-22T09:05:21.000Z",
      "arch": "x86_64",
      "commit": "7085f8116810f29f596111a333281b4fe92eb431",
      "fileid": "3d6efb40ada49e27f3390f43222cdee5948ed4839e4bc6f86981be1ac4653df0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/24769770699"
    }
  ]
}