{
  "_id": "6aca7c41fe5cc25786e8a08d",
  "Package": "GSALightning",
  "Type": "Package",
  "Title": "Fast Permutation-based Gene Set Analysis",
  "Version": "1.40.0",
  "Date": "2015-12-30",
  "Author": "Billy Heung Wing Chang",
  "Maintainer": "Billy Heung Wing Chang <billyheungwing@gmail.com>",
  "Description": "GSALightning provides a fast implementation of\npermutation-based gene set analysis for two-sample problem.\nThis package is particularly useful when testing simultaneously\na large number of gene sets, or when a large number of\npermutations is necessary for more accurate p-values\nestimation.",
  "License": "GPL (>=2)",
  "URL": "https://github.com/billyhw/GSALightning",
  "BugReports": "https://github.com/billyhw/GSALightning/issues",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, BiologicalQuestion, GeneSetEnrichment,\nDifferentialExpression, GeneExpression, Transcription",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-10 16:28:38 UTC",
    "User": "root"
  },
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:42:25 UTC",
  "RemoteUrl": "https://github.com/bioc/GSALightning",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "26045721597eda7f0d2b07c7fbad8ec608a4082d",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "GSALightning_1.40.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/15e022753ce583308436b33c742610bd72d11a668fa95c0d55fdf82567be5dbc",
  "_filesize": 4300144,
  "_sha256": "15e022753ce583308436b33c742610bd72d11a668fa95c0d55fdf82567be5dbc",
  "_expires": "2027-01-18T17:56:15.000Z",
  "_created": "2026-10-10T16:28:38.000Z",
  "_published": "2026-10-10T17:56:17.766Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38067567781",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 1,
    "warning": 4,
    "note": 10
  },
  "_upstream": "https://github.com/bioc/GSALightning",
  "_commit": {
    "id": "26045721597eda7f0d2b07c7fbad8ec608a4082d",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380145
  },
  "_maintainer": {
    "name": "Billy Heung Wing Chang",
    "email": "billyheungwing@gmail.com",
    "login": "billyhw",
    "description": "",
    "uuid": 9052109
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 114259026212,
      "time": 129,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11676111271"
    },
    {
      "job": 114259026286,
      "time": 165,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11675691627"
    },
    {
      "job": 114259026266,
      "time": 166,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11675541944"
    },
    {
      "job": 114259026304,
      "time": 93,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11678191041"
    },
    {
      "job": 114259026227,
      "time": 119,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11678221049"
    },
    {
      "job": 114258290105,
      "time": 223,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11675846204"
    },
    {
      "job": 114259026222,
      "time": 85,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11675936317"
    },
    {
      "job": 114259026235,
      "time": 85,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11675611596"
    },
    {
      "job": 114259026360,
      "time": 79,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11675730719"
    },
    {
      "job": 114259026317,
      "time": 76,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11675851328"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3.0",
      "role": "Depends"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "software",
    "biologicalquestion",
    "genesetenrichment",
    "differentialexpression",
    "geneexpression",
    "transcription"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "billyhw",
      "count": 203,
      "uuid": 9052109
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 423,
    "source": "https://www.bioconductor.org/packages/stats/bioc/GSALightning"
  },
  "_devurl": "https://github.com/billyhw/gsalightning",
  "_searchresults": 5,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GSALightning.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/billyhw/gsalightning",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "GSALight",
    "permTestLight",
    "wilcoxTest"
  ],
  "_datasets": [
    {
      "name": "expression",
      "title": "Breast Cancer Data from The Cancer Genome Atlas (TCGA)",
      "object": "expression",
      "file": "expression.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 909,
      "table": true,
      "tojson": true
    },
    {
      "name": "sampleInfo",
      "title": "Sample Information for the Breast Cancer Data from The Cancer Genome Atlas (TCGA)",
      "object": "sampleInfo",
      "file": "sampleInfo.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "exp.ID",
        "TN"
      ],
      "rows": 1218,
      "table": true,
      "tojson": true
    },
    {
      "name": "targetGenes",
      "title": "Target Genes of Distal Regulatory Elements",
      "object": "targetGenes",
      "file": "targetGenes.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "GSALightning-package",
      "title": "Fast Permutation-based Gene Set Analysis",
      "topics": [
        "GSALightning-package",
        "GSALightning"
      ]
    },
    {
      "page": "expression",
      "title": "Breast Cancer Data from The Cancer Genome Atlas (TCGA)",
      "topics": [
        "expression"
      ]
    },
    {
      "page": "GSALight",
      "title": "Fast Permutation-based Gene Set Analysis",
      "topics": [
        "GSALight"
      ]
    },
    {
      "page": "permTestLight",
      "title": "Fast Single-Gene Permutation Test",
      "topics": [
        "permTestLight"
      ]
    },
    {
      "page": "sampleInfo",
      "title": "Sample Information for the Breast Cancer Data from The Cancer Genome Atlas (TCGA)",
      "topics": [
        "sampleInfo"
      ]
    },
    {
      "page": "targetGenes",
      "title": "Target Genes of Distal Regulatory Elements",
      "topics": [
        "targetGenes"
      ]
    },
    {
      "page": "wilcoxTest",
      "title": "Single-Gene Mann Whitney Wilcoxon Test",
      "topics": [
        "wilcoxTest"
      ]
    }
  ],
  "_rundeps": [
    "data.table",
    "lattice",
    "Matrix"
  ],
  "_vignettes": [
    {
      "source": "vignette.Rmd",
      "filename": "vignette.html",
      "title": "GSALightning: Ultra-fast Permutation-based Gene Set Analysis",
      "author": "Billy Heung Wing Chang",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Introduction",
        "2. Installation and Quick Start",
        "2.1 Installing GSALightning",
        "2.2 Running GSALightning",
        "3. The Inputs for GSALight()",
        "4. GSALight()",
        "4.1 Preliminiary Data Check",
        "4.2 Most Commonly Considered Arguments for GSALight()",
        "4.3 The Maxmean, Mean, and Absolute Mean Statistics",
        "4.4 Outputs of GSALight()",
        "4.5 Default Number of Permutations",
        "4.6 Restandardization",
        "5. Other Functions in GSALightning",
        "5.1 Single Gene Permutation Test",
        "5.2 Mann-Whitney U Test for Single Gene Testing",
        "5.3 Gene Set Analysis for Paired Design",
        "References"
      ],
      "created": "2016-01-07 18:53:22",
      "modified": "2016-06-13 16:01:46",
      "commits": 3
    }
  ],
  "_score": 4,
  "_indexed": false,
  "_nocasepkg": "gsalightning",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/GSALightning",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.40.0",
      "date": "2026-10-10T16:31:27.000Z",
      "distro": "resolute",
      "commit": "26045721597eda7f0d2b07c7fbad8ec608a4082d",
      "fileid": "https://r2.ropensci.org/286e6c73f039c64f9af3c8a3f86e47ecbcc0509efc0f8badd624c8707336dacd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38067567781"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.40.0",
      "date": "2026-10-10T16:31:17.000Z",
      "distro": "resolute",
      "commit": "26045721597eda7f0d2b07c7fbad8ec608a4082d",
      "fileid": "https://r2.ropensci.org/79f9b9eee0047635015fb12c568589e19f3247cc2d9a9a57af97c52324cdeea5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38067567781"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.40.0",
      "date": "2026-10-10T17:55:13.000Z",
      "commit": "26045721597eda7f0d2b07c7fbad8ec608a4082d",
      "fileid": "https://r2.ropensci.org/0b9532d4862ce9b3e2c4fa71a7b608f6073db9fc70258be2bb704cfc2dded3f8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38067567781"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.40.0",
      "date": "2026-10-10T17:55:25.000Z",
      "commit": "26045721597eda7f0d2b07c7fbad8ec608a4082d",
      "fileid": "https://r2.ropensci.org/f092fd82469847932a7cb37bdde889781fc7e87f06c0987420822aa7af0562d6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38067567781"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.40.0",
      "date": "2026-10-10T16:30:28.000Z",
      "commit": "26045721597eda7f0d2b07c7fbad8ec608a4082d",
      "fileid": "https://r2.ropensci.org/305c5010a642e07545efc5817bf701a4645f6132959f863c0cd638d1b93b5ffc",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38067567781"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.40.0",
      "date": "2026-10-10T16:29:52.000Z",
      "commit": "26045721597eda7f0d2b07c7fbad8ec608a4082d",
      "fileid": "https://r2.ropensci.org/980880d7edc16a0f0029d8cd0652480d26542276b6101445e32d465daf2ef2b6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38067567781"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.40.0",
      "date": "2026-10-10T16:29:52.000Z",
      "commit": "26045721597eda7f0d2b07c7fbad8ec608a4082d",
      "fileid": "https://r2.ropensci.org/fa2cb84e6b067d5a4e48858ec31a7b503b975df4c4833038ac131c875fe167ae",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38067567781"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.40.0",
      "date": "2026-10-10T16:29:49.000Z",
      "commit": "26045721597eda7f0d2b07c7fbad8ec608a4082d",
      "fileid": "https://r2.ropensci.org/866eb1bf17ace518e72033219af7c27685cbc196d067d9a2475c7955932486ac",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38067567781"
    }
  ]
}