{
  "_id": "6a496f1e355ae3ef1c537c2f",
  "Package": "RTopper",
  "Type": "Package",
  "Title": "This package is designed to perform Gene Set Analysis across\nmultiple genomic platforms",
  "Version": "1.43.1",
  "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://marchionnilab.r-universe.dev",
  "Date/Publication": "2022-10-25 15:32:51 UTC",
  "RemoteUrl": "https://github.com/marchionniLab/RTopper",
  "RemoteRef": "HEAD",
  "RemoteSha": "e8eb4a54500fd591f3867a9c41094748195473df",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 20:29:16 UTC",
    "User": "root"
  },
  "_user": "marchionnilab",
  "_type": "src",
  "_file": "RTopper_1.43.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/1dd8618af1274f0f3e4eedff4b93a59776b5f74fe22b86436ded2c11c8fe10e9",
  "_filesize": 1391302,
  "_sha256": "1dd8618af1274f0f3e4eedff4b93a59776b5f74fe22b86436ded2c11c8fe10e9",
  "_expires": "2026-10-12T20:37:48.000Z",
  "_created": "2026-07-04T20:29:16.000Z",
  "_published": "2026-07-04T20:37:50.008Z",
  "_jobs": [
    {
      "job": 85164576917,
      "time": 180,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8085192911"
    },
    {
      "job": 85164576908,
      "time": 181,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8085192999"
    },
    {
      "job": 85164576913,
      "time": 113,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8085184996"
    },
    {
      "job": 85164576919,
      "time": 116,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8085185511"
    },
    {
      "job": 85164302993,
      "time": 238,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8085170925"
    },
    {
      "job": 85164576905,
      "time": 119,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8085185941"
    },
    {
      "job": 85164576939,
      "time": 457,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8085225992"
    },
    {
      "job": 85164576926,
      "time": 395,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8085218938"
    },
    {
      "job": 85164576930,
      "time": 472,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8085227786"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/marchionnilab/actions/runs/28718621094",
  "_status": "success",
  "_upstream": "https://github.com/marchionniLab/RTopper",
  "_commit": {
    "id": "e8eb4a54500fd591f3867a9c41094748195473df",
    "author": "claudio.zanettini <claudio.zanettini@gmail.com>",
    "committer": "claudio.zanettini <claudio.zanettini@gmail.com>",
    "message": "fix: version bump\n",
    "time": 1666711971
  },
  "_maintainer": {
    "name": "Luigi Marchionni",
    "email": "marchion@jhu.edu",
    "login": "marchion",
    "description": "",
    "uuid": 1276265
  },
  "_distro": "resolute",
  "_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": "marchionnilab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.59.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.58.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microarray"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "dtenenba",
      "count": 24,
      "uuid": 2286826
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "c1au6i0",
      "count": 5,
      "uuid": 47305205
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "marchion",
      "count": 1,
      "uuid": 1276265
    }
  ],
  "_userbio": {
    "uuid": 74625328,
    "type": "organization",
    "name": "Marchionni Lab",
    "followers": 7
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RTopper"
  },
  "_devurl": "https://github.com/marchionnilab/rtopper",
  "_searchresults": 9,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/RTopper.html",
    "LICENSE",
    "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"
  ],
  "_vignettes": [
    {
      "source": "RTopper.Rnw",
      "filename": "RTopper.pdf",
      "title": "RTopper user's manual",
      "engine": "utils::Sweave",
      "headings": [
        "Overview",
        "RTopper data structure",
        "Data analysis with RTopper",
        "System Information",
        "References"
      ],
      "created": "2013-11-01 20:20:41",
      "modified": "2022-10-25 15:32:51",
      "commits": 5
    }
  ],
  "_score": 3.6989700043360187,
  "_indexed": false,
  "_nocasepkg": "rtopper",
  "_universes": [
    "marchionnilab"
  ],
  "_indexurl": "https://bioc.r-universe.dev/RTopper",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.43.1",
      "date": "2026-07-04T20:31:48.000Z",
      "distro": "resolute",
      "commit": "e8eb4a54500fd591f3867a9c41094748195473df",
      "fileid": "https://r2.ropensci.org/f6b328b4a9e4f25142c6a1f099da2865e7a909118635b8076df5d95baeb424f8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/marchionnilab/actions/runs/28718621094"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.43.1",
      "date": "2026-07-04T20:31:52.000Z",
      "distro": "resolute",
      "commit": "e8eb4a54500fd591f3867a9c41094748195473df",
      "fileid": "https://r2.ropensci.org/724ad9490a3c212283d930957193f9e50c54dbff1c8fd94d8e3366c0ce831fb2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/marchionnilab/actions/runs/28718621094"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.43.1",
      "date": "2026-07-04T20:30:58.000Z",
      "commit": "e8eb4a54500fd591f3867a9c41094748195473df",
      "fileid": "https://r2.ropensci.org/0e3a4ee1b7e35dcb68a60a57f7aa77009ef9dfab32985baaee4aa940b98ca8db",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/marchionnilab/actions/runs/28718621094"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.43.1",
      "date": "2026-07-04T20:31:01.000Z",
      "commit": "e8eb4a54500fd591f3867a9c41094748195473df",
      "fileid": "https://r2.ropensci.org/99ede27aa8550f2bbe3ca77a610f41dcb3dc787ef6c34704755c8ecac9dc3853",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/marchionnilab/actions/runs/28718621094"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.43.1",
      "date": "2026-07-04T20:31:33.000Z",
      "commit": "e8eb4a54500fd591f3867a9c41094748195473df",
      "fileid": "https://r2.ropensci.org/f5c7dbb6a0f57e6342e9f4486866050ca19919bbbe34621655aa64faeb66297a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/marchionnilab/actions/runs/28718621094"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.43.1",
      "date": "2026-07-04T20:36:18.000Z",
      "commit": "e8eb4a54500fd591f3867a9c41094748195473df",
      "fileid": "https://r2.ropensci.org/e47d8df0c15c90ba9734b5697f67f7c5ab44a044d47facf229868185028b740a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/marchionnilab/actions/runs/28718621094"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.43.1",
      "date": "2026-07-04T20:35:24.000Z",
      "commit": "e8eb4a54500fd591f3867a9c41094748195473df",
      "fileid": "https://r2.ropensci.org/c9cc067a7c89b505cc567176deceb5df9c7bef7a4626e47950a0f58f83746fdc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/marchionnilab/actions/runs/28718621094"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.43.1",
      "date": "2026-07-04T20:36:35.000Z",
      "commit": "e8eb4a54500fd591f3867a9c41094748195473df",
      "fileid": "https://r2.ropensci.org/f8bd45a0798c9c8c65747914e2327ee7920011346ec1e99e4f9c30b604b6cbb8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/marchionnilab/actions/runs/28718621094"
    }
  ]
}