{
  "_id": "6a1b01a71d7bb097a0a007ba",
  "Package": "RTopper",
  "Type": "Package",
  "Title": "This package is designed to perform Gene Set Analysis across\nmultiple genomic platforms",
  "Version": "1.59.0",
  "Date": "2011-09-14",
  "Author": "Luigi Marchionni <marchion@jhu.edu>, Svitlana Tyekucheva\n<svitlana@jimmy.harvard.edu>",
  "Maintainer": "Luigi Marchionni <marchion@jhu.edu>",
  "Description": "the RTopper package is designed to perform and integrate\ngene set enrichment results across multiple genomic platforms.",
  "License": "GPL (>= 3) + file LICENSE",
  "biocViews": "Microarray",
  "LazyLoad": "yes",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:35:47 UTC",
  "RemoteUrl": "https://github.com/bioc/RTopper",
  "RemoteRef": "HEAD",
  "RemoteSha": "41b97ec4956e9196337cccc6c01fd6451020f9d5",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:57:08 UTC",
    "User": "root"
  },
  "MD5sum": "017db590e8a897122cb1916788d3cc75",
  "_user": "bioc",
  "_type": "src",
  "_file": "RTopper_1.59.0.tar.gz",
  "_fileid": "080ad4e0471738308786f250dbac7c9e6d8ad3d143183a3507587c516f278b4b",
  "_filesize": 1250961,
  "_sha256": "080ad4e0471738308786f250dbac7c9e6d8ad3d143183a3507587c516f278b4b",
  "_created": "2026-05-30T09:57:08.000Z",
  "_published": "2026-05-30T15:26:31.142Z",
  "_jobs": [
    {
      "job": 78641108543,
      "time": 166,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307602960"
    },
    {
      "job": 78641108549,
      "time": 238,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307609537"
    },
    {
      "job": 78641108557,
      "time": 231,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307608893"
    },
    {
      "job": 78641108556,
      "time": 162,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7309232976"
    },
    {
      "job": 78641108561,
      "time": 116,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7309228162"
    },
    {
      "job": 78640036941,
      "time": 462,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307347983"
    },
    {
      "job": 78641108544,
      "time": 136,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307600112"
    },
    {
      "job": 78641108588,
      "time": 412,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307626924"
    },
    {
      "job": 78641108612,
      "time": 379,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7307623854"
    },
    {
      "job": 78641108564,
      "time": 380,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307623992"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 2,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677260625",
  "_status": "failure",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/RTopper",
  "_commit": {
    "id": "41b97ec4956e9196337cccc6c01fd6451020f9d5",
    "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": 1777379747
  },
  "_maintainer": {
    "name": "Luigi Marchionni",
    "email": "marchion@jhu.edu",
    "login": "marchion",
    "description": "",
    "uuid": 1276265
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.12.0",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "multtest",
      "role": "Imports"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "KEGGREST",
      "role": "Suggests"
    },
    {
      "package": "GO.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": "1.59.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.58.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microarray"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 500,
    "source": "https://www.bioconductor.org/packages/stats/bioc/RTopper"
  },
  "_mentions": 1,
  "_searchresults": 12,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/RTopper.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "adjustPvalGSE",
    "combineGSE",
    "computeDrStat",
    "convertToDr",
    "runBatchGSE"
  ],
  "_datasets": [
    {
      "name": "dat",
      "title": "A test dataset for the RTopper package",
      "object": "exampleData",
      "file": "exampleData.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "fgsList",
      "title": "A list of Functional Gene Set (FGS) to be used to run the examples in the RTopper package",
      "object": "fgsList",
      "file": "fgsList.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "gseResultsSep",
      "title": "A list of separated gene set enrichment p-values to be used to run the examples in the RTopper package",
      "object": "gseResultsSep",
      "file": "gseResultsSep.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "intScores",
      "title": "A list of genomic scores integrated across distinct data sets to be used to run the examples in the RTopper package",
      "object": "intScores",
      "file": "intScores.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "pheno",
      "title": "A test dataset for the RTopper package",
      "object": "exampleData",
      "file": "exampleData.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Sample",
        "Class"
      ],
      "rows": 95,
      "table": true,
      "tojson": true
    },
    {
      "name": "sepScores",
      "title": "A list of separate gene-to-phenotype association scores, obtained indipendently for each distinct data set to be used to run the examples in the RTopper package",
      "object": "sepScores",
      "file": "sepScores.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "RTopper-package",
      "title": "A package to perform run Gene Set Enrichment across genomic platforms",
      "topics": [
        "RTopper-package",
        "RTopper"
      ]
    },
    {
      "page": "adjustPvalGSE",
      "title": "Multiple testing correction",
      "topics": [
        "adjustPvalGSE"
      ]
    },
    {
      "page": "combineGSE",
      "title": "Combines GSE results",
      "topics": [
        "combineGSE"
      ]
    },
    {
      "page": "computeDrStat",
      "title": "Computes gene-to-phenotype associations scores",
      "topics": [
        "computeDrStat"
      ]
    },
    {
      "page": "convertToDr",
      "title": "Converts genomic data to a list suitable for computing gene-to-phenotype scores",
      "topics": [
        "convertToDr"
      ]
    },
    {
      "page": "dat",
      "title": "A test dataset for the RTopper package",
      "topics": [
        "dat"
      ]
    },
    {
      "page": "fgsList",
      "title": "A list of Functional Gene Set (FGS) to be used to run the examples in the RTopper package",
      "topics": [
        "fgsList"
      ]
    },
    {
      "page": "gseResultsSep",
      "title": "A list of separated gene set enrichment p-values to be used to run the examples in the RTopper package",
      "topics": [
        "gseResultsSep"
      ]
    },
    {
      "page": "intScores",
      "title": "A list of genomic scores integrated across distinct data sets to be used to run the examples in the RTopper package",
      "topics": [
        "intScores"
      ]
    },
    {
      "page": "pheno",
      "title": "A test dataset for the RTopper package",
      "topics": [
        "pheno"
      ]
    },
    {
      "page": "runBatchGSE",
      "title": "To perform GSE analysis over multipple experiments and functional themes",
      "topics": [
        "runBatchGSE"
      ]
    },
    {
      "page": "sepScores",
      "title": "A list of separate gene-to-phenotype association scores, obtained indipendently for each distinct data set to be used to run the examples in the RTopper package",
      "topics": [
        "sepScores"
      ]
    }
  ],
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "generics",
    "lattice",
    "limma",
    "MASS",
    "Matrix",
    "multtest",
    "statmod",
    "survival"
  ],
  "_score": 2.3802112417116064,
  "_indexed": true,
  "_nocasepkg": "rtopper",
  "_universes": [
    "bioc",
    "marchion"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.59.0",
      "date": "2026-05-30T10:44:24.000Z",
      "distro": "noble",
      "commit": "41b97ec4956e9196337cccc6c01fd6451020f9d5",
      "fileid": "8f33231e7791faeef27cc054c81b4c0e4e56690a3e5666044c3d51182d60edd1",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677260625"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.59.0",
      "date": "2026-05-30T10:44:27.000Z",
      "distro": "noble",
      "commit": "41b97ec4956e9196337cccc6c01fd6451020f9d5",
      "fileid": "80446bb51d32c470de85dc2b15c2b9a01df26172d4786a37effc787f7de6f486",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677260625"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.59.0",
      "date": "2026-05-30T15:25:26.000Z",
      "commit": "41b97ec4956e9196337cccc6c01fd6451020f9d5",
      "fileid": "74017629d67f2df1baa51378ecacb8aac4c68a8a67fdd5a52793a9b037c5bd96",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677260625"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.59.0",
      "date": "2026-05-30T15:24:54.000Z",
      "commit": "41b97ec4956e9196337cccc6c01fd6451020f9d5",
      "fileid": "b89bdc7a1baf0cbe632ff5ae8c43e9172f9167b344c0d74996ba2ddfaa0bf619",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677260625"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.59.0",
      "date": "2026-05-30T10:43:28.000Z",
      "commit": "41b97ec4956e9196337cccc6c01fd6451020f9d5",
      "fileid": "66f9c4e76a94dc94751d4a31b250715c5e4ebc326dd4325a9991fa9583521d3e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677260625"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.59.0",
      "date": "2026-05-30T10:47:12.000Z",
      "commit": "41b97ec4956e9196337cccc6c01fd6451020f9d5",
      "fileid": "39367a07528758267f07f34c5774bc9e99e6758d5292a26fc916196af7887394",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677260625"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.59.0",
      "date": "2026-05-30T10:46:49.000Z",
      "commit": "41b97ec4956e9196337cccc6c01fd6451020f9d5",
      "fileid": "c74243c99c7d55e9a3521e0f534f614c350b489138b5631873f14cb58f54ceba",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677260625"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.59.0",
      "date": "2026-05-30T10:46:50.000Z",
      "commit": "41b97ec4956e9196337cccc6c01fd6451020f9d5",
      "fileid": "3854ed5a4f7416c9ed85226abb24bfae424d0993400f3d032ca564f7096ad612",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677260625"
    }
  ]
}