{
  "_id": "6a37c2813efcd9bda442d27d",
  "Package": "ClassComparison",
  "Version": "3.3.5",
  "Date": "2025-02-04",
  "Title": "Classes and Methods for \"Class Comparison\" Problems on\nMicroarrays",
  "Authors@R": "person(given = c(\"Kevin\", \"R.\"),\nfamily = \"Coombes\",\nrole = c(\"aut\", \"cre\"),\nemail = \"krc@silicovore.com\")",
  "Description": "Defines the classes used for \"class comparison\" problems\nin the OOMPA project (<http://oompa.r-forge.r-project.org/>).\nClass comparison includes tests for differential expression;\nsee Simon's book for details on typical problem types.",
  "License": "Apache License (== 2.0)",
  "LazyLoad": "yes",
  "biocViews": "Microarray, DifferentialExpression, MultipleComparisons",
  "URL": "http://oompa.r-forge.r-project.org/",
  "Repository": "https://r-forge.r-universe.dev",
  "Date/Publication": "2026-05-22 18:40:06 UTC",
  "RemoteUrl": "https://github.com/r-forge/oompa",
  "RemoteRef": "HEAD",
  "RemoteSha": "969e77c65694e77068421e66612b9fc687a5a023",
  "RemoteSubdir": "pkg/ClassComparison",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-21 10:49:29 UTC",
    "User": "root"
  },
  "Author": "Kevin R. Coombes [aut, cre]",
  "Maintainer": "Kevin R. Coombes <krc@silicovore.com>",
  "MD5sum": "e3fbc467bcab43d8cb7c59007e5b183e",
  "_user": "r-forge",
  "_type": "src",
  "_file": "ClassComparison_3.3.5.tar.gz",
  "_fileid": "d554b93555fd255a1b76306001c57b5160a22e3bdf95836408668007be7cb2d6",
  "_filesize": 887562,
  "_sha256": "d554b93555fd255a1b76306001c57b5160a22e3bdf95836408668007be7cb2d6",
  "_created": "2026-06-21T10:49:29.000Z",
  "_published": "2026-06-21T10:52:49.921Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 82563707657,
      "time": 165,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7774562168"
    },
    {
      "job": 82563707673,
      "time": 157,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7774561371"
    },
    {
      "job": 82563707666,
      "time": 119,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7774557153"
    },
    {
      "job": 82563707671,
      "time": 74,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7774552484"
    },
    {
      "job": 82563535207,
      "time": 169,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7774543350"
    },
    {
      "job": 82563707653,
      "time": 111,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7774556097"
    },
    {
      "job": 82563707668,
      "time": 82,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7774553028"
    },
    {
      "job": 82563707675,
      "time": 75,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7774552267"
    },
    {
      "job": 82563707677,
      "time": 101,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7774555182"
    }
  ],
  "_buildurl": "https://github.com/r-universe/r-forge/actions/runs/27901880242",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/r-forge/oompa",
  "_commit": {
    "id": "969e77c65694e77068421e66612b9fc687a5a023",
    "author": "krcoombes (Kevin Coombes) <kevin.r.coombes@gmail.com>",
    "committer": "krcoombes (Kevin Coombes) <kevin.r.coombes@gmail.com>",
    "message": "Added XKCD color names.\n\ngit-svn-id: svn://svn.r-forge.r-project.org/svnroot/oompa@707 edb9625f-4e0d-4859-8d74-9fd3b1da38cb\n",
    "time": 1779475206
  },
  "_maintainer": {
    "name": "Kevin R. Coombes",
    "email": "krc@silicovore.com"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0",
      "role": "Depends"
    },
    {
      "package": "oompaBase",
      "version": ">= 3.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "splines",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    }
  ],
  "_owner": "r-forge",
  "_selfowned": true,
  "_usedby": 3,
  "_updates": [
    {
      "week": "2025-36",
      "n": 1
    },
    {
      "week": "2025-40",
      "n": 1
    },
    {
      "week": "2025-45",
      "n": 2
    },
    {
      "week": "2025-46",
      "n": 1
    },
    {
      "week": "2025-47",
      "n": 2
    },
    {
      "week": "2026-02",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 8
    },
    {
      "week": "2026-19",
      "n": 6
    },
    {
      "week": "2026-21",
      "n": 1
    }
  ],
  "_tags": [],
  "_topics": [
    "microarray",
    "differentialexpression",
    "multiplecomparisons"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "krcoombes",
      "count": 582,
      "uuid": 5930440
    },
    {
      "user": "lmsstudios",
      "count": 101,
      "uuid": 97995137
    },
    {
      "user": "yamachan18",
      "count": 19,
      "uuid": 81639585
    },
    {
      "user": "theussl",
      "count": 1,
      "uuid": 22165873
    }
  ],
  "_userbio": {
    "uuid": 75573726,
    "type": "organization",
    "name": " R-Forge",
    "followers": 27,
    "description": "git-svn mirrors from R-Forge"
  },
  "_downloads": {
    "count": 333,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ClassComparison"
  },
  "_mentions": 2,
  "_devurl": "https://github.com/r-forge/oompa",
  "_searchresults": 47,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/ClassComparison.html",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/r-forge/oompa",
  "_realowner": "r-forge",
  "_cranurl": true,
  "_releases": [
    {
      "version": "3.1.5",
      "date": "2017-07-11"
    },
    {
      "version": "3.1.6",
      "date": "2018-05-17"
    },
    {
      "version": "3.1.7",
      "date": "2019-04-23"
    },
    {
      "version": "3.1.8",
      "date": "2019-05-06"
    },
    {
      "version": "3.3.2",
      "date": "2024-08-17"
    },
    {
      "version": "3.3.5",
      "date": "2025-02-05"
    }
  ],
  "_exports": [
    "anova",
    "as.data.frame",
    "Bum",
    "countSignificant",
    "cutoffSignificant",
    "Dudoit",
    "dwil",
    "hist",
    "image",
    "likelihoodBum",
    "MultiLinearModel",
    "MultiTtest",
    "MultiTtestPaired",
    "MultiTtestUnequal",
    "multiTukey",
    "MultiWilcoxonTest",
    "plot",
    "probDiff",
    "rankSum",
    "Sam",
    "selectSignificant",
    "show",
    "SingleGroup",
    "SmoothTtest",
    "summary",
    "TNoM",
    "TwoGroupStats",
    "update"
  ],
  "_help": [
    {
      "page": "cc00-0-Bum-class",
      "title": "Class \"Bum\"",
      "topics": [
        "Bum",
        "Bum-class",
        "countSignificant,Bum-method",
        "cutoffSignificant,Bum-method",
        "hist,Bum-method",
        "image,Bum-method",
        "likelihoodBum",
        "selectSignificant,Bum-method",
        "summary,Bum-method"
      ]
    },
    {
      "page": "cc00-1-BumSummary-class",
      "title": "Class \"BumSummary\"",
      "topics": [
        "BumSummary",
        "BumSummary-class",
        "show,BumSummary-method"
      ]
    },
    {
      "page": "cc04-0-Dudoit-class",
      "title": "Class \"Dudoit\"",
      "topics": [
        "countSignificant,Dudoit-method",
        "cutoffSignificant,Dudoit-method",
        "Dudoit",
        "Dudoit-class",
        "plot,Dudoit,missing-method",
        "selectSignificant,Dudoit-method"
      ]
    },
    {
      "page": "cc02-1-dwil",
      "title": "Wilcoxon Density Function",
      "topics": [
        "dwil"
      ]
    },
    {
      "page": "cc03-0-MultiLinearModel-class",
      "title": "Class \"MultiLinearModel\"",
      "topics": [
        "anova,MultiLinearModel-method",
        "as.data.frame,MultiLinearModel-method",
        "hist,MultiLinearModel-method",
        "MultiLinearModel",
        "MultiLinearModel-class",
        "multiTukey",
        "plot,MultiLinearModel,ANY-method",
        "plot,MultiLinearModel,missing-method",
        "summary,MultiLinearModel-method"
      ]
    },
    {
      "page": "cc01-0-MultiTtest-class",
      "title": "Class \"MultiTtest\"",
      "topics": [
        "as.data.frame,MultiTtest-method",
        "hist,MultiTtest-method",
        "MultiTtest",
        "MultiTtest-class",
        "plot,MultiTtest,ANY-method",
        "plot,MultiTtest,missing-method",
        "summary,MultiTtest-method"
      ]
    },
    {
      "page": "cc02-0-MultiWilcoxonTest-class",
      "title": "Class \"MultiWilcoxonTest\"",
      "topics": [
        "countSignificant,MultiWilcoxonTest-method",
        "cutoffSignificant,MultiWilcoxonTest-method",
        "hist,MultiWilcoxonTest-method",
        "MultiWilcoxonTest",
        "MultiWilcoxonTest-class",
        "plot,MultiWilcoxonTest,missing-method",
        "probDiff,MultiWilcoxonTest-method",
        "selectSignificant,MultiWilcoxonTest-method",
        "summary,MultiWilcoxonTest-method"
      ]
    },
    {
      "page": "cc02-2-rankSum",
      "title": "Wilcoxon Rank-Sum Statistic",
      "topics": [
        "rankSum"
      ]
    },
    {
      "page": "cc06-0-Sam-class",
      "title": "Class \"Sam\"",
      "topics": [
        "countSignificant,Sam-method",
        "plot,Sam,missing-method",
        "Sam",
        "Sam-class",
        "selectSignificant,Sam-method",
        "summary,Sam-method"
      ]
    },
    {
      "page": "cc06-1-SamSummary-class",
      "title": "Class \"SamSummary\"",
      "topics": [
        "SamSummary",
        "SamSummary-class",
        "show,SamSummary-method"
      ]
    },
    {
      "page": "cc00-2-significant-method",
      "title": "Generic Methods for Significance",
      "topics": [
        "countSignificant",
        "countSignificant,ANY-method",
        "countSignificant-method",
        "cutoffSignificant",
        "cutoffSignificant,ANY-method",
        "cutoffSignificant-method",
        "probDiff",
        "probDiff,ANY-method",
        "probDiff-method",
        "selectSignificant",
        "selectSignificant,ANY-method",
        "selectSignificant-method"
      ]
    },
    {
      "page": "cc08-0-SingleGroup-class",
      "title": "Class \"SingleGroup\"",
      "topics": [
        "as.data.frame,SingleGroup-method",
        "plot,SingleGroup,missing-method",
        "print,SingleGroup-method",
        "show,SingleGroup-method",
        "SingleGroup",
        "SingleGroup-class",
        "summary,SingleGroup-method"
      ]
    },
    {
      "page": "cc09-0-SmoothTtest-class",
      "title": "Class \"SmoothTtest\"",
      "topics": [
        "as.data.frame,SmoothTtest-method",
        "plot,SmoothTtest,missing-method",
        "SmoothTtest",
        "SmoothTtest-class",
        "summary,SmoothTtest-method"
      ]
    },
    {
      "page": "cc05-0-TNoM-class",
      "title": "Classes \"TNoM\" and \"fullTNoM\"",
      "topics": [
        "countSignificant,TNoM-method",
        "fullTNoM-class",
        "hist,fullTNoM-method",
        "plot,fullTNoM,missing-method",
        "selectSignificant,TNoM-method",
        "summary,TNoM-method",
        "TNoM",
        "TNoM-class",
        "update,TNoM-method"
      ]
    },
    {
      "page": "cc05-1-TNoMSummary-class",
      "title": "Class \"TNoMSummary\"",
      "topics": [
        "show,TNoMSummary-method",
        "TNoMSummary",
        "TNoMSummary-class"
      ]
    },
    {
      "page": "cc07-0-TwoGroupStats-class",
      "title": "Class \"TwoGroupStats\"",
      "topics": [
        "as.data.frame,TwoGroupStats-method",
        "plot,TwoGroupStats,missing-method",
        "print,TwoGroupStats-method",
        "show,TwoGroupStats-method",
        "summary,TwoGroupStats-method",
        "TwoGroupStats",
        "TwoGroupStats-class"
      ]
    },
    {
      "page": "cc01-1-variantT-class",
      "title": "Classes for Variant T-tests",
      "topics": [
        "MultiTtestPaired",
        "MultiTtestPaired-class",
        "MultiTtestUnequal",
        "MultiTtestUnequal-class",
        "summary,MultiTtestPaired-method",
        "summary,MultiTtestUnequal-method"
      ]
    }
  ],
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "cluster",
    "generics",
    "oompaBase"
  ],
  "_vignettes": [
    {
      "source": "oompa-cc.Rnw",
      "filename": "oompa-cc.pdf",
      "title": "OOMPA ClassComparison",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "Getting Started",
        "Gene-by-gene t-tests",
        "Beta-uniform mixture models to account for multiple testing",
        "Wilcoxon rank sum tests and empirical Bayes",
        "Permutation based methods",
        "Significance Analysis of Microarrays",
        "Other class comparison approaches"
      ],
      "created": "2014-02-10 15:51:10",
      "modified": "2014-05-05 19:51:49",
      "commits": 2
    }
  ],
  "_score": 6.358734127198011,
  "_indexed": true,
  "_nocasepkg": "classcomparison",
  "_universes": [
    "r-forge"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.3.5",
      "date": "2026-06-21T10:52:07.000Z",
      "distro": "noble",
      "commit": "969e77c65694e77068421e66612b9fc687a5a023",
      "fileid": "f5fbffa80eb59d88c18ef92eb50d10cb1af9c068bc84e07c3a21f76e9589f83b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/r-forge/actions/runs/27901880242"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "3.3.5",
      "date": "2026-06-21T10:51:59.000Z",
      "distro": "noble",
      "commit": "969e77c65694e77068421e66612b9fc687a5a023",
      "fileid": "2cab71f4c30b9a6280172a28e7ae922b09f2afea13dba7ec7600c23164bd6061",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/r-forge/actions/runs/27901880242"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.3.5",
      "date": "2026-06-21T10:51:29.000Z",
      "commit": "969e77c65694e77068421e66612b9fc687a5a023",
      "fileid": "cdfa529680b2a77e9d3eaf884797160d1c67b4d883093d1186694dfb926b3058",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/r-forge/actions/runs/27901880242"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "3.3.5",
      "date": "2026-06-21T10:50:52.000Z",
      "commit": "969e77c65694e77068421e66612b9fc687a5a023",
      "fileid": "d894869845f6bc773d63c10dd6b30ccd105fa427a84b5c0e2f77afc5f02ea49c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/r-forge/actions/runs/27901880242"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "3.3.5",
      "date": "2026-06-21T10:51:41.000Z",
      "commit": "969e77c65694e77068421e66612b9fc687a5a023",
      "fileid": "259df99d6c0032fabf82201bc562caa44d2c4398330c1afddcffe5e723e0fd7f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/r-forge/actions/runs/27901880242"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "3.3.5",
      "date": "2026-06-21T10:50:36.000Z",
      "commit": "969e77c65694e77068421e66612b9fc687a5a023",
      "fileid": "dd4c23e02455fa8c09a33e33f4e8e9b237f096ece1526621040dcc1da3f6da73",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/r-forge/actions/runs/27901880242"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "3.3.5",
      "date": "2026-06-21T10:50:39.000Z",
      "commit": "969e77c65694e77068421e66612b9fc687a5a023",
      "fileid": "cef8dfba4b18c45708b8069b511d2dd09b2fb1f615c9f895806ae10e0107c21b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/r-forge/actions/runs/27901880242"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "3.3.5",
      "date": "2026-06-21T10:51:02.000Z",
      "commit": "969e77c65694e77068421e66612b9fc687a5a023",
      "fileid": "fa0deb9e3b8317ba887b2f8c143a0c2b44d8124742ac0980af200e2cb2f9a540",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/r-forge/actions/runs/27901880242"
    }
  ]
}