{
  "_id": "6a493ccaa19c9318096e7224",
  "Package": "cnvGSA",
  "Type": "Package",
  "Title": "Gene Set Analysis of (Rare) Copy Number Variants",
  "Version": "1.57.0",
  "Date": "2015-03-02",
  "Author": "Daniele Merico <daniele.merico@gmail.com>, Robert Ziman\n<rziman@gmail.com>; packaged by Joseph Lugo\n<joseph.r.lugo@gmail.com>",
  "Maintainer": "Joseph Lugo <joseph.r.lugo@gmail.com>",
  "Description": "This package is intended to facilitate gene-set\nassociation with rare CNVs in case-control studies.",
  "License": "LGPL",
  "LazyLoad": "yes",
  "biocViews": "MultipleComparison",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:36:25 UTC",
  "RemoteUrl": "https://github.com/bioc/cnvGSA",
  "RemoteRef": "HEAD",
  "RemoteSha": "b8915b8630fcaca20dbc67e0c0e38c642a29b481",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 00:31:04 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "cnvGSA_1.57.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/fbc3ed88fb70c1b1fbbacfb5ae8a8ea0882c5a5ae78977cb436131960394eb31",
  "_filesize": 366720,
  "_sha256": "fbc3ed88fb70c1b1fbbacfb5ae8a8ea0882c5a5ae78977cb436131960394eb31",
  "_expires": "2026-10-12T17:03:04.000Z",
  "_created": "2026-07-04T00:31:04.000Z",
  "_published": "2026-07-04T17:03:06.013Z",
  "_bioccheck": {
    "error": 2,
    "warning": 4,
    "note": 13
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28689274662",
  "_status": "success",
  "_upstream": "https://github.com/bioc/cnvGSA",
  "_commit": {
    "id": "b8915b8630fcaca20dbc67e0c0e38c642a29b481",
    "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": 1777379785
  },
  "_maintainer": {
    "name": "Joseph Lugo",
    "email": "joseph.r.lugo@gmail.com",
    "login": "joelugo",
    "description": "",
    "uuid": 116655856
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85150497269,
      "time": 217,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8076617478"
    },
    {
      "job": 85150497091,
      "time": 194,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8076614387"
    },
    {
      "job": 85150497210,
      "time": 239,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8076620289"
    },
    {
      "job": 85150497114,
      "time": 154,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8076608634"
    },
    {
      "job": 85150497109,
      "time": 117,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8076603643"
    },
    {
      "job": 85150496999,
      "time": 181,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8076587707"
    },
    {
      "job": 85150497199,
      "time": 134,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8076605949"
    },
    {
      "job": 85150497108,
      "time": 507,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8076657552"
    },
    {
      "job": 85150497270,
      "time": 498,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8076656284"
    },
    {
      "job": 85150497287,
      "time": 535,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8076661578"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "brglm",
      "role": "Depends"
    },
    {
      "package": "doParallel",
      "role": "Depends"
    },
    {
      "package": "foreach",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "splitstackshape",
      "role": "Depends"
    },
    {
      "package": "cnvGSAdata",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.57.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.56.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "multiplecomparison"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_searchresults": 4,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/cnvGSA.html",
    "extra/contents.json",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "cnvData.ls",
    "cnvData.ls<-",
    "cnvGSAgsTables",
    "cnvGSAIn",
    "CnvGSAInput",
    "cnvGSAlogRegTest",
    "CnvGSAOutput",
    "config.ls",
    "config.ls<-",
    "f.enrFiles",
    "f.makeViz",
    "f.readConfig",
    "geneID.ls",
    "geneID.ls<-",
    "gsData.ls",
    "gsData.ls<-",
    "gsTables.ls",
    "params.ls",
    "params.ls<-",
    "phData.ls",
    "phData.ls<-",
    "res.ls"
  ],
  "_help": [
    {
      "page": "cnvGSA-package",
      "title": "Gene-set Analysis of (Rare) Copy Number Variants",
      "topics": [
        "cnvGSA-package",
        "cnvGSA"
      ]
    },
    {
      "page": "cnvGSAgsTables",
      "title": "Creates the gene-set tables for each gene-set.",
      "topics": [
        "cnvGSAgsTables"
      ]
    },
    {
      "page": "cnvGSAIn",
      "title": "Creating the input S4 object needed to run the script.",
      "topics": [
        "cnvGSAIn"
      ]
    },
    {
      "page": "CnvGSAInput-class",
      "title": "Class '\"CnvGSAInput\"'",
      "topics": [
        "cnvData.ls",
        "cnvData.ls,CnvGSAInput-method",
        "cnvData.ls<-",
        "cnvData.ls<-,CnvGSAInput-method",
        "CnvGSAInput",
        "CnvGSAInput-class",
        "config.ls",
        "config.ls,CnvGSAInput-method",
        "config.ls<-",
        "config.ls<-,CnvGSAInput-method",
        "geneID.ls",
        "geneID.ls,CnvGSAInput-method",
        "geneID.ls<-",
        "geneID.ls<-,CnvGSAInput-method",
        "gsData.ls",
        "gsData.ls,CnvGSAInput-method",
        "gsData.ls<-",
        "gsData.ls<-,CnvGSAInput-method",
        "params.ls",
        "params.ls,CnvGSAInput-method",
        "params.ls<-",
        "params.ls<-,CnvGSAInput-method",
        "phData.ls",
        "phData.ls,CnvGSAInput-method",
        "phData.ls<-",
        "phData.ls<-,CnvGSAInput-method"
      ]
    },
    {
      "page": "cnvGSAlogRegTest",
      "title": "Performing the logistic regression tests on the CNV data.",
      "topics": [
        "cnvGSAlogRegTest"
      ]
    },
    {
      "page": "CnvGSAOutput-class",
      "title": "Class '\"CnvGSAOutput\"'",
      "topics": [
        "CnvGSAOutput",
        "CnvGSAOutput-class",
        "gsData.ls,CnvGSAOutput-method",
        "gsTables.ls",
        "gsTables.ls,CnvGSAOutput-method",
        "phData.ls,CnvGSAOutput-method",
        "res.ls",
        "res.ls,CnvGSAOutput-method"
      ]
    },
    {
      "page": "f.enrFiles",
      "title": "Prepares the files for the enrichment maps.",
      "topics": [
        "f.enrFiles"
      ]
    },
    {
      "page": "f.makeViz",
      "title": "Creates the plots from the CnvGSAOutput data.",
      "topics": [
        "f.makeViz"
      ]
    },
    {
      "page": "f.readConfig",
      "title": "Reading in the config file.",
      "topics": [
        "f.readConfig"
      ]
    }
  ],
  "_rundeps": [
    "BiocGenerics",
    "brglm",
    "codetools",
    "data.table",
    "doParallel",
    "foreach",
    "generics",
    "GenomicRanges",
    "IRanges",
    "iterators",
    "profileModel",
    "S4Vectors",
    "Seqinfo",
    "splitstackshape"
  ],
  "_vignettes": [
    {
      "source": "cnvGSA-vignette.Rnw",
      "filename": "cnvGSA-vignette.pdf",
      "title": "cnvGSA - Gene-Set Analysis of Rare Copy Number Variants",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 20:25:15",
      "modified": "2015-04-13 15:30:27",
      "commits": 5
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "cnvgsa",
  "_universes": [
    "bioc",
    "joelugo"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.57.0",
      "date": "2026-07-04T00:33:53.000Z",
      "distro": "resolute",
      "commit": "b8915b8630fcaca20dbc67e0c0e38c642a29b481",
      "fileid": "https://r2.ropensci.org/dd69240ed08a96888c1f21881286692901d623463c83bf957760f2be95234ce2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28689274662"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.57.0",
      "date": "2026-07-04T00:34:36.000Z",
      "distro": "resolute",
      "commit": "b8915b8630fcaca20dbc67e0c0e38c642a29b481",
      "fileid": "https://r2.ropensci.org/44fb6b08ff9bb80e48640a17099a6f2c26ea279616a041fa42db5fc70c4469d5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28689274662"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.57.0",
      "date": "2026-07-04T00:33:18.000Z",
      "commit": "b8915b8630fcaca20dbc67e0c0e38c642a29b481",
      "fileid": "https://r2.ropensci.org/a6c482422a05403095e27f9a16e6d4fd6266b96319e204cfc522fb4f7914c0a3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28689274662"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.57.0",
      "date": "2026-07-04T00:32:47.000Z",
      "commit": "b8915b8630fcaca20dbc67e0c0e38c642a29b481",
      "fileid": "https://r2.ropensci.org/7ed7d513a11bc4ed8f0ffb712360bd5797dbaf1706eae44f157eb9196f52c8d2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28689274662"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.57.0",
      "date": "2026-07-04T00:33:33.000Z",
      "commit": "b8915b8630fcaca20dbc67e0c0e38c642a29b481",
      "fileid": "https://r2.ropensci.org/6a254ee373470838a52fd59d2db79969a1005b5fc9c1a74db3fbcde8e0f8a1de",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28689274662"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.57.0",
      "date": "2026-07-04T00:38:57.000Z",
      "commit": "b8915b8630fcaca20dbc67e0c0e38c642a29b481",
      "fileid": "https://r2.ropensci.org/15627e97d580ec82f12a27f9e6c8b57c701bfbb81adceeda6b679ab8905e100c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28689274662"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.57.0",
      "date": "2026-07-04T00:38:51.000Z",
      "commit": "b8915b8630fcaca20dbc67e0c0e38c642a29b481",
      "fileid": "https://r2.ropensci.org/e433fb3eb5fe404e9f0895b4bfc91e4b4bbd8c545e965b162a23fd273132c0f2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28689274662"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.57.0",
      "date": "2026-07-04T00:39:25.000Z",
      "commit": "b8915b8630fcaca20dbc67e0c0e38c642a29b481",
      "fileid": "https://r2.ropensci.org/f5f18437bd2a8f6f8a4a61d9ee67eed26565d1d3fc774283500c229f6cbf7180",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28689274662"
    }
  ]
}