{
  "_id": "6abcdc9999f7aa8c6aa4d267",
  "Package": "PADOG",
  "Version": "1.55.0",
  "Date": "2020-1-31",
  "Title": "Pathway Analysis with Down-weighting of Overlapping Genes\n(PADOG)",
  "Author": "Adi Laurentiu Tarca <atarca@med.wayne.edu>; Zhonghui Xu\n<zhonghui.xu@gmail.com>",
  "Maintainer": "Adi L. Tarca <atarca@med.wayne.edu>",
  "Description": "This package implements a general purpose gene set\nanalysis method called PADOG that downplays the importance of\ngenes that apear often accross the sets of genes to be\nanalyzed. The package provides also a benchmark for gene set\nanalysis methods in terms of sensitivity and ranking using 24\npublic datasets from KEGGdzPathwaysGEO package.",
  "License": "GPL (>= 2)",
  "URL": "",
  "Collate": "padog.R compPADOG.R filteranot.R",
  "LazyLoad": "yes",
  "biocViews": "Microarray, OneChannel, TwoChannel",
  "Config/pak/sysreqs": "libpng-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:36:43 UTC",
  "RemoteUrl": "https://github.com/bioc/PADOG",
  "RemoteRef": "HEAD",
  "RemoteSha": "8d85cf2b04d18d0c81c24616135f3fd16e1fd043",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-30 09:26:27 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "PADOG_1.55.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/323cafed4755dd258016a3b945c72fa47a2eb058255a8dad2d084663f14c3391",
  "_filesize": 356011,
  "_sha256": "323cafed4755dd258016a3b945c72fa47a2eb058255a8dad2d084663f14c3391",
  "_expires": "2027-01-08T09:55:35.000Z",
  "_created": "2026-09-30T09:26:27.000Z",
  "_published": "2026-09-30T09:55:37.430Z",
  "_bioccheck": {
    "error": 1,
    "warning": 4,
    "note": 16
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/36695363951",
  "_status": "success",
  "_upstream": "https://github.com/bioc/PADOG",
  "_commit": {
    "id": "8d85cf2b04d18d0c81c24616135f3fd16e1fd043",
    "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": 1777379803
  },
  "_maintainer": {
    "name": "Adi L. Tarca",
    "email": "atarca@med.wayne.edu"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 109824569151,
      "time": 218,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11087298471"
    },
    {
      "job": 109824569203,
      "time": 399,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11087408896"
    },
    {
      "job": 109824569213,
      "time": 431,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11087508766"
    },
    {
      "job": 109824569122,
      "time": 174,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11089192550"
    },
    {
      "job": 109824569302,
      "time": 179,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11088628421"
    },
    {
      "job": 109822225530,
      "time": 401,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11087432761"
    },
    {
      "job": 109824569242,
      "time": 166,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11087108809"
    },
    {
      "job": 109824569216,
      "time": 247,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11088316872"
    },
    {
      "job": 109824569320,
      "time": 219,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11087938258"
    },
    {
      "job": 109824569375,
      "time": 234,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11087669598"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "KEGGdzPathwaysGEO",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "GSA",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "doRNG",
      "role": "Imports"
    },
    {
      "package": "hgu133plus2.db",
      "role": "Imports"
    },
    {
      "package": "hgu133a.db",
      "role": "Imports"
    },
    {
      "package": "KEGGREST",
      "role": "Imports"
    },
    {
      "package": "nlme",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Suggests"
    },
    {
      "package": "parallel",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.55.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.54.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microarray",
    "onechannel",
    "twochannel"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 470,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 708,
    "source": "https://www.bioconductor.org/packages/stats/bioc/PADOG"
  },
  "_mentions": 19,
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/PADOG.html"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "compPADOG",
    "filteranot",
    "padog"
  ],
  "_help": [
    {
      "page": "compPADOG",
      "title": "Benchmark for gene set analysis methods using 24 datasets",
      "topics": [
        "compPADOG"
      ]
    },
    {
      "page": "filteranot",
      "title": "Remove duplicate probesets/probes from an gene expression matrix based on p-values from a moderated t-test, in order to apply a gene set analysis.",
      "topics": [
        "filteranot"
      ]
    },
    {
      "page": "padog",
      "title": "Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)",
      "topics": [
        "padog"
      ]
    }
  ],
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "digest",
    "doRNG",
    "fastmap",
    "foreach",
    "generics",
    "glue",
    "GSA",
    "hgu133a.db",
    "hgu133plus2.db",
    "httr",
    "IRanges",
    "iterators",
    "jsonlite",
    "KEGGdzPathwaysGEO",
    "KEGGREST",
    "lattice",
    "lifecycle",
    "limma",
    "memoise",
    "mime",
    "nlme",
    "openssl",
    "org.Hs.eg.db",
    "pkgconfig",
    "png",
    "R6",
    "rlang",
    "rngtools",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "statmod",
    "sys",
    "vctrs",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "PADOG.Rnw",
      "filename": "PADOG.pdf",
      "title": "PADOG",
      "engine": "utils::Sweave",
      "headings": [
        "Overview",
        "Pathway / gene set analysis with PADOG package",
        "Benchmark of gene set analysis methods"
      ],
      "created": "2013-11-01 20:26:34",
      "modified": "2023-11-04 01:36:10",
      "commits": 5
    }
  ],
  "_score": 5.079181246047625,
  "_indexed": true,
  "_nocasepkg": "padog",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.55.0",
      "date": "2026-09-30T09:31:19.000Z",
      "distro": "resolute",
      "commit": "8d85cf2b04d18d0c81c24616135f3fd16e1fd043",
      "fileid": "https://r2.ropensci.org/ae1c2ca23ee528a1d945141caced0ee38c6080c8f2acd2e781f12aea6ea873da",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695363951"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.55.0",
      "date": "2026-09-30T09:31:50.000Z",
      "distro": "resolute",
      "commit": "8d85cf2b04d18d0c81c24616135f3fd16e1fd043",
      "fileid": "https://r2.ropensci.org/42f76772b293f07b6e5ed749e75e626ed327f1592ec845174fb9e2ff1c648910",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695363951"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.55.0",
      "date": "2026-09-30T09:53:34.000Z",
      "commit": "8d85cf2b04d18d0c81c24616135f3fd16e1fd043",
      "fileid": "https://r2.ropensci.org/c98508be9d30120a1ae1ed2f7bc7fe9480dd8a87335ef98f901cc93557e4a421",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695363951"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.55.0",
      "date": "2026-09-30T09:53:41.000Z",
      "commit": "8d85cf2b04d18d0c81c24616135f3fd16e1fd043",
      "fileid": "https://r2.ropensci.org/363c87699f4a90fb4a858f6919ddffdb7c886225ef56ea1dd0cfccf896dd680b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695363951"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.55.0",
      "date": "2026-09-30T09:29:39.000Z",
      "commit": "8d85cf2b04d18d0c81c24616135f3fd16e1fd043",
      "fileid": "https://r2.ropensci.org/432c5d591b8fc448ec17208394fe6a5b128845e3719beb4517e065be537d185f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695363951"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-09-30T09:28:54.000Z",
      "commit": "8d85cf2b04d18d0c81c24616135f3fd16e1fd043",
      "fileid": "https://r2.ropensci.org/bac879fbd7af0a2a268b12781c3542c91e0f086623e7c2e714b666e1c3013ff5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695363951"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-09-30T09:28:22.000Z",
      "commit": "8d85cf2b04d18d0c81c24616135f3fd16e1fd043",
      "fileid": "https://r2.ropensci.org/c9ed814e9f3cb239150bef6609db789cb00c0e6fa4b4289beb8685acd195a643",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695363951"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-09-30T09:28:26.000Z",
      "commit": "8d85cf2b04d18d0c81c24616135f3fd16e1fd043",
      "fileid": "https://r2.ropensci.org/60edf2534321c1ba185e2e0fcbb3ec4e05ece1f30e5de005ccae0bc04a1cb3ce",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36695363951"
    }
  ]
}