{
  "_id": "6aab8c003d719c1f8406b7a8",
  "Package": "plgem",
  "Title": "Detect differential expression in microarray and proteomics\ndatasets with the Power Law Global Error Model (PLGEM)",
  "Version": "1.85.0",
  "Author": "Mattia Pelizzola <mattia.pelizzola@gmail.com> and Norman\nPavelka <normanpavelka@gmail.com>",
  "Description": "The Power Law Global Error Model (PLGEM) has been shown to\nfaithfully model the variance-versus-mean dependence that\nexists in a variety of genome-wide datasets, including\nmicroarray and proteomics data. The use of PLGEM has been shown\nto improve the detection of differentially expressed genes or\nproteins in these datasets.",
  "Maintainer": "Norman Pavelka <normanpavelka@gmail.com>",
  "License": "GPL-2",
  "URL": "http://www.genopolis.it",
  "biocViews": "ImmunoOncology, Microarray, DifferentialExpression,\nProteomics, GeneExpression, MassSpectrometry",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:31:01 UTC",
  "RemoteUrl": "https://github.com/bioc/plgem",
  "RemoteRef": "HEAD",
  "RemoteSha": "01627314fc19651d8ce05de8585e2a2e8f695957",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-17 06:38:17 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "plgem_1.85.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/b9f567633a65736501a6fc1ded9ce80e1ae0cd3a2c117d8e65e57b4882a162f7",
  "_filesize": 1131842,
  "_sha256": "b9f567633a65736501a6fc1ded9ce80e1ae0cd3a2c117d8e65e57b4882a162f7",
  "_expires": "2026-12-26T06:43:10.000Z",
  "_created": "2026-09-17T06:38:17.000Z",
  "_published": "2026-09-17T06:43:12.742Z",
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 13
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35190519322",
  "_status": "success",
  "_upstream": "https://github.com/bioc/plgem",
  "_commit": {
    "id": "01627314fc19651d8ce05de8585e2a2e8f695957",
    "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": 1777379461
  },
  "_maintainer": {
    "name": "Norman Pavelka",
    "email": "normanpavelka@gmail.com",
    "login": "normanpavelka",
    "description": "",
    "uuid": 34261575
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 105102535380,
      "time": 144,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "10484210464"
    },
    {
      "job": 105102535432,
      "time": 180,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10484018207"
    },
    {
      "job": 105102535457,
      "time": 247,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10483558251"
    },
    {
      "job": 105102535485,
      "time": 98,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10484058128"
    },
    {
      "job": 105102535373,
      "time": 120,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10483163436"
    },
    {
      "job": 105101922760,
      "time": 160,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10483068450"
    },
    {
      "job": 105102535390,
      "time": 102,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10484145799"
    },
    {
      "job": 105102535478,
      "time": 82,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10484220311"
    },
    {
      "job": 105102535455,
      "time": 89,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10484235293"
    },
    {
      "job": 105102535557,
      "time": 73,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10484190420"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "version": ">= 2.5.5",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.85.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.84.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "microarray",
    "differentialexpression",
    "proteomics",
    "geneexpression",
    "massspectrometry"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 467,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 670,
    "source": "https://www.bioconductor.org/packages/stats/bioc/plgem"
  },
  "_mentions": 4,
  "_searchresults": 10,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/plgem.html"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "plgem.deg",
    "plgem.fit",
    "plgem.obsStn",
    "plgem.pValue",
    "plgem.resampledStn",
    "plgem.write.summary",
    "run.plgem",
    "setGpar"
  ],
  "_datasets": [
    {
      "name": "LPSeset",
      "title": "ExpressionSet for Testing PLGEM",
      "object": "LPSeset",
      "file": "LPSeset.rda",
      "class": [
        "ExpressionSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "LPSeset",
      "title": "ExpressionSet for Testing PLGEM",
      "topics": [
        "LPSeset"
      ]
    },
    {
      "page": "plgem.deg",
      "title": "Selection of Differentially Expressed Genes/Proteins With PLGEM",
      "topics": [
        "plgem.deg"
      ]
    },
    {
      "page": "plgem.fit",
      "title": "PLGEM Fitting and Evaluation",
      "topics": [
        "plgem.fit"
      ]
    },
    {
      "page": "plgem.obsStn",
      "title": "Computation of Observed PLGEM-STN Statistics",
      "topics": [
        "plgem.obsStn"
      ]
    },
    {
      "page": "plgem.pValue",
      "title": "Computation of PLGEM p-values",
      "topics": [
        "plgem.pValue"
      ]
    },
    {
      "page": "plgem.resampledStn",
      "title": "Computation of Resampled PLGEM-STN Statistics",
      "topics": [
        "plgem.resampledStn"
      ]
    },
    {
      "page": "plgem.write.summary",
      "title": "Write the Result of a PLGEM Analysis to the Working Directory",
      "topics": [
        "plgem.write.summary"
      ]
    },
    {
      "page": "run.plgem",
      "title": "Wrapper for Power Law Global Error Model (PLGEM) analysis method",
      "topics": [
        "run.plgem"
      ]
    },
    {
      "page": "setGpar",
      "title": "Set graphical parameters for PLGEM fitting evaluation plots",
      "topics": [
        "setGpar"
      ]
    }
  ],
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "generics",
    "MASS"
  ],
  "_vignettes": [
    {
      "source": "plgem.Rnw",
      "filename": "plgem.pdf",
      "title": "An introduction to PLGEM",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-02-06 11:18:29",
      "modified": "2013-02-06 11:18:29",
      "commits": 1
    }
  ],
  "_score": 4.380211241711606,
  "_indexed": true,
  "_nocasepkg": "plgem",
  "_universes": [
    "bioc",
    "normanpavelka"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.85.0",
      "date": "2026-09-17T06:41:25.000Z",
      "distro": "resolute",
      "commit": "01627314fc19651d8ce05de8585e2a2e8f695957",
      "fileid": "https://r2.ropensci.org/b3df4c0f4972e2a9cb23be2eaff866bd8a9bb7c1f48105cc112193cd4f30a720",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35190519322"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.85.0",
      "date": "2026-09-17T06:42:26.000Z",
      "distro": "resolute",
      "commit": "01627314fc19651d8ce05de8585e2a2e8f695957",
      "fileid": "https://r2.ropensci.org/ec9e532893a5da67b8d20dd195ba438984e87c8ebe0c4a30f913cf3cbaaf4c6b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35190519322"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.85.0",
      "date": "2026-09-17T06:40:39.000Z",
      "commit": "01627314fc19651d8ce05de8585e2a2e8f695957",
      "fileid": "https://r2.ropensci.org/47d6110dd617628f3287ecd28b234cc6e4e523fb9260dda017c74dc0a89b361c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35190519322"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.85.0",
      "date": "2026-09-17T06:40:53.000Z",
      "commit": "01627314fc19651d8ce05de8585e2a2e8f695957",
      "fileid": "https://r2.ropensci.org/a3192ab1570de61500f6aab8b86958d26cbe81c6f5cdf7fe2a8879c049813f85",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35190519322"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.85.0",
      "date": "2026-09-17T06:40:21.000Z",
      "commit": "01627314fc19651d8ce05de8585e2a2e8f695957",
      "fileid": "https://r2.ropensci.org/49c9c500b50c3535d8a8f62a0a40e56b67b1e2a9bfd41e802416678ccce9323d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35190519322"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.85.0",
      "date": "2026-09-17T06:39:25.000Z",
      "commit": "01627314fc19651d8ce05de8585e2a2e8f695957",
      "fileid": "https://r2.ropensci.org/9e95aade6b7310adb97c05e387b6ef6f76fc8ea7531cc86198930b05cfcf4795",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35190519322"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.85.0",
      "date": "2026-09-17T06:39:32.000Z",
      "commit": "01627314fc19651d8ce05de8585e2a2e8f695957",
      "fileid": "https://r2.ropensci.org/c2450db704b36de72a8c0b46a530d725b20f0d2b9518d06018f9c1b2d6e29112",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35190519322"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.85.0",
      "date": "2026-09-17T06:39:21.000Z",
      "commit": "01627314fc19651d8ce05de8585e2a2e8f695957",
      "fileid": "https://r2.ropensci.org/fae16aad16c38cac165f7130339bd53e70f1c8d92158a05eea6cb27391751170",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35190519322"
    }
  ]
}