{
  "_id": "6a4798762f27a93436c0fcfe",
  "Package": "KOGMWU",
  "Type": "Package",
  "Title": "Functional Summary and Meta-Analysis of Gene Expression Data",
  "Version": "1.2",
  "Date": "2019-02-19",
  "Author": "Mikhail V. Matz",
  "Maintainer": "Mikhail V. Matz <matz@utexas.edu>",
  "Description": "Rank-based tests for enrichment of KOG (euKaryotic\nOrthologous Groups) classes with up- or down-regulated genes\nbased on a continuous measure. The meta-analysis is based on\ncorrelation of KOG delta-ranks across datasets (delta-rank is\nthe difference between mean rank of genes belonging to a KOG\nclass and mean rank of all other genes). With binary measure (1\nor 0 to indicate significant and non-significant genes),\none-tailed Fisher's exact test for over-representation of each\nKOG class among significant genes will be performed.",
  "License": "GPL-3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-03 08:32:35 UTC",
    "User": "root"
  },
  "Repository": "https://z0on.r-universe.dev",
  "Date/Publication": "2019-02-19 18:00:03 UTC",
  "RemoteUrl": "https://github.com/cran/KOGMWU",
  "RemoteRef": "HEAD",
  "RemoteSha": "6ac264c08e17ac8736f70e58da62f9fa91af032c",
  "_user": "z0on",
  "_type": "src",
  "_file": "KOGMWU_1.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/a54b758e0ad4e18b79cfd97afb10ef59a1d439b2ed048e71486fefe9b50a15fb",
  "_filesize": 937032,
  "_sha256": "a54b758e0ad4e18b79cfd97afb10ef59a1d439b2ed048e71486fefe9b50a15fb",
  "_expires": "2026-10-11T11:09:41.000Z",
  "_created": "2026-07-03T08:32:35.000Z",
  "_published": "2026-07-03T11:09:42.410Z",
  "_jobs": [
    {
      "job": 84987363949,
      "time": 117,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8061738904"
    },
    {
      "job": 84987364012,
      "time": 114,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8061738231"
    },
    {
      "job": 84987364002,
      "time": 205,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8061754845"
    },
    {
      "job": 84987363948,
      "time": 134,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8061734688"
    },
    {
      "job": 84987363480,
      "time": 171,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8061697920"
    },
    {
      "job": 84987364093,
      "time": 99,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8061732774"
    },
    {
      "job": 84987363944,
      "time": 65,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8061721123"
    },
    {
      "job": 84987364090,
      "time": 59,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8061719336"
    },
    {
      "job": 84987363959,
      "time": 73,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8061723635"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/z0on/actions/runs/28648484080",
  "_status": "success",
  "_upstream": "https://github.com/cran/KOGMWU",
  "_commit": {
    "id": "6ac264c08e17ac8736f70e58da62f9fa91af032c",
    "author": "Mikhail V. Matz <matz@utexas.edu>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.2\n",
    "time": 1550599203
  },
  "_maintainer": {
    "name": "Mikhail V. Matz",
    "email": "matz@utexas.edu",
    "login": "z0on",
    "twitter": "@heatshok",
    "description": "https://scholar.google.com/citations?user=VB83XasAAAAJ&hl=en ",
    "uuid": 7553944
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "pheatmap",
      "role": "Depends"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "z0on",
      "count": 3,
      "uuid": 7553944
    }
  ],
  "_userbio": {
    "uuid": 7553944,
    "type": "user",
    "name": "Mikhail V Matz",
    "followers": 105,
    "description": "https://scholar.google.com/citations?user=VB83XasAAAAJ&hl=en "
  },
  "_downloads": {
    "count": 274,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/KOGMWU"
  },
  "_mentions": 1,
  "_searchresults": 17,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/KOGMWU.html",
    "manual.pdf"
  ],
  "_realowner": "z0on",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0",
      "date": "2015-03-05"
    },
    {
      "version": "1.1",
      "date": "2016-11-17"
    },
    {
      "version": "1.2",
      "date": "2019-02-19"
    }
  ],
  "_exports": [
    "corrPlot",
    "kog.ft",
    "kog.mwu",
    "kog.mwut",
    "makeDeltaRanksTable",
    "panel.cor",
    "panel.cor.pval"
  ],
  "_datasets": [
    {
      "name": "adults.3dHeat.logFoldChange",
      "title": "Heat stress response of adult coral",
      "object": "adults.3dHeat.logFoldChange",
      "file": "adults.3dHeat.logFoldChange.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gene",
        "lfc"
      ],
      "rows": 44363,
      "table": true,
      "tojson": true
    },
    {
      "name": "gene2kog",
      "title": "KOG class annotations",
      "object": "gene2kog",
      "file": "gene2kog.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2"
      ],
      "rows": 16175,
      "table": true,
      "tojson": true
    },
    {
      "name": "larvae.longTerm",
      "title": "Long-term heat stress response of coral larvae",
      "object": "larvae.longTerm",
      "file": "larvae.longTerm.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gene",
        "lfc"
      ],
      "rows": 31844,
      "table": true,
      "tojson": true
    },
    {
      "name": "larvae.shortTerm",
      "title": "Short-term heat stress response of coral larvae",
      "object": "larvae.shortTerm",
      "file": "larvae.shortTerm.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gene",
        "lfc"
      ],
      "rows": 32307,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "KOGMWU-package",
      "title": "Functional summary and meta-analysis of gene expression data",
      "topics": [
        "KOGMWU-package",
        "KOGMWU"
      ]
    },
    {
      "page": "adults.3dHeat.logFoldChange",
      "title": "Heat stress response of adult coral",
      "topics": [
        "adults.3dHeat.logFoldChange"
      ]
    },
    {
      "page": "corrPlot",
      "title": "Plots a pairwise correlation with linear regression line",
      "topics": [
        "corrPlot"
      ]
    },
    {
      "page": "gene2kog",
      "title": "KOG class annotations",
      "topics": [
        "gene2kog"
      ]
    },
    {
      "page": "kog.ft",
      "title": "One-tailed Fisher's exact test for KOG enrichment.",
      "topics": [
        "kog.ft"
      ]
    },
    {
      "page": "kog.mwu",
      "title": "Tests for KOG class enrichment.",
      "topics": [
        "kog.mwu"
      ]
    },
    {
      "page": "kog.mwut",
      "title": "Mann-Whitney U test for KOG enrichment.",
      "topics": [
        "kog.mwut"
      ]
    },
    {
      "page": "larvae.longTerm",
      "title": "Long-term heat stress response of coral larvae",
      "topics": [
        "larvae.longTerm"
      ]
    },
    {
      "page": "larvae.shortTerm",
      "title": "Short-term heat stress response of coral larvae",
      "topics": [
        "larvae.shortTerm"
      ]
    },
    {
      "page": "makeDeltaRanksTable",
      "title": "Make a combined delta-ranks table from several kog.mwu() results.",
      "topics": [
        "makeDeltaRanksTable"
      ]
    },
    {
      "page": "panel.cor",
      "title": "accessory function for pairs() to display Pearson correlations",
      "topics": [
        "panel.cor"
      ]
    },
    {
      "page": "panel.cor.pval",
      "title": "accessory function for pairs() to display pvalue of the Pearson correlation",
      "topics": [
        "panel.cor.pval"
      ]
    }
  ],
  "_rundeps": [
    "cli",
    "farver",
    "glue",
    "gtable",
    "labeling",
    "lifecycle",
    "pheatmap",
    "R6",
    "RColorBrewer",
    "rlang",
    "scales",
    "viridisLite"
  ],
  "_score": 1.2304489213782739,
  "_indexed": true,
  "_nocasepkg": "kogmwu",
  "_universes": [
    "z0on"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2",
      "date": "2026-07-03T08:34:33.000Z",
      "distro": "resolute",
      "commit": "6ac264c08e17ac8736f70e58da62f9fa91af032c",
      "fileid": "https://r2.ropensci.org/66a1ab2f6222a6e285a28341150494a84bf64a16b7552e50a883cc175b0e7011",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/z0on/actions/runs/28648484080"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.2",
      "date": "2026-07-03T08:34:31.000Z",
      "distro": "resolute",
      "commit": "6ac264c08e17ac8736f70e58da62f9fa91af032c",
      "fileid": "https://r2.ropensci.org/72a7fa32cc9b1b3c9db14decad8e74f7be587e8fdc71ab7e82d4e355ae047745",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/z0on/actions/runs/28648484080"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2",
      "date": "2026-07-03T08:35:27.000Z",
      "commit": "6ac264c08e17ac8736f70e58da62f9fa91af032c",
      "fileid": "https://r2.ropensci.org/800d819b212bd60181123d0d8b6e04a97e63f7ac6b6e5b8fb5d711dac8711a5a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/z0on/actions/runs/28648484080"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.2",
      "date": "2026-07-03T08:34:26.000Z",
      "commit": "6ac264c08e17ac8736f70e58da62f9fa91af032c",
      "fileid": "https://r2.ropensci.org/7e7785066b4b8685cf4afd71e8f2bbea3cd1564c361804264d73677ae2220650",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/z0on/actions/runs/28648484080"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2",
      "date": "2026-07-03T08:34:31.000Z",
      "commit": "6ac264c08e17ac8736f70e58da62f9fa91af032c",
      "fileid": "https://r2.ropensci.org/2d2f5b55960a2c57c638de300310661446adfd405b808dc57469e3bf41140adc",
      "status": "success",
      "buildurl": "https://github.com/r-universe/z0on/actions/runs/28648484080"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2",
      "date": "2026-07-03T08:33:37.000Z",
      "commit": "6ac264c08e17ac8736f70e58da62f9fa91af032c",
      "fileid": "https://r2.ropensci.org/cc3ebd5315cd5b589673a7660791c116aa952701619dd5c9bf176bce8f6c4c61",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/z0on/actions/runs/28648484080"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2",
      "date": "2026-07-03T08:33:34.000Z",
      "commit": "6ac264c08e17ac8736f70e58da62f9fa91af032c",
      "fileid": "https://r2.ropensci.org/aa19fa428fd6d2a205f51cc567927023f2d99ec9c03a7fc9844a91a6ccbf5786",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/z0on/actions/runs/28648484080"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.2",
      "date": "2026-07-03T08:33:44.000Z",
      "commit": "6ac264c08e17ac8736f70e58da62f9fa91af032c",
      "fileid": "https://r2.ropensci.org/d8ef93f40554432a56a86df5da8705371c2650fce6cf6850b785036a6f86d4d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/z0on/actions/runs/28648484080"
    }
  ]
}