{
  "_id": "6a499a634ae8ee07ee132f8d",
  "Package": "limmaGUI",
  "Version": "1.89.0",
  "Date": "2018-09-28",
  "Title": "GUI for limma Package With Two Color Microarrays",
  "Author": "James Wettenhall [aut], Gordon Smyth [aut], Keith Satterley\n[ctb]",
  "Maintainer": "Gordon Smyth <smyth@wehi.edu.au>",
  "Description": "A Graphical User Interface for differential expression\nanalysis of two-color microarray data using the limma package.",
  "License": "GPL (>=2)",
  "URL": "http://bioinf.wehi.edu.au/limmaGUI/",
  "biocViews": "GUI, GeneExpression, DifferentialExpression, DataImport,\nBayesian, Regression, TimeCourse, Microarray, mRNAMicroarray,\nTwoChannel, BatchEffect, MultipleComparison, Normalization,\nPreprocessing, QualityControl",
  "Config/pak/sysreqs": "libx11-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:30:34 UTC",
  "RemoteUrl": "https://github.com/bioc/limmaGUI",
  "RemoteRef": "HEAD",
  "RemoteSha": "d80f056590f52caaf5aa59b032e5bd2a7a986297",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 23:37:50 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "limmaGUI_1.89.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/e16805f5b8db443480f395c3dd31df58cd79760a25bf32106812574c74cf0b05",
  "_filesize": 5607262,
  "_sha256": "e16805f5b8db443480f395c3dd31df58cd79760a25bf32106812574c74cf0b05",
  "_expires": "2026-10-12T23:42:25.000Z",
  "_created": "2026-07-04T23:37:50.000Z",
  "_published": "2026-07-04T23:42:27.835Z",
  "_bioccheck": {
    "error": 2,
    "warning": 5,
    "note": 15
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28723204780",
  "_status": "success",
  "_upstream": "https://github.com/bioc/limmaGUI",
  "_commit": {
    "id": "d80f056590f52caaf5aa59b032e5bd2a7a986297",
    "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": 1777379434
  },
  "_maintainer": {
    "name": "Gordon Smyth",
    "email": "smyth@wehi.edu.au",
    "login": "gksmyth",
    "description": "Head of the Bioinformatics Division, WEHI",
    "uuid": 30491078
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85176219143,
      "time": 171,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8086453621"
    },
    {
      "job": 85176219167,
      "time": 170,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8086453616"
    },
    {
      "job": 85176219162,
      "time": 231,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8086459528"
    },
    {
      "job": 85176219142,
      "time": 90,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8086445873"
    },
    {
      "job": 85176219160,
      "time": 96,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8086446392"
    },
    {
      "job": 85176048628,
      "time": 192,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8086437203"
    },
    {
      "job": 85176219138,
      "time": 107,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 85176219174,
      "time": 96,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8086446295"
    },
    {
      "job": 85176219172,
      "time": 84,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8086445358"
    },
    {
      "job": 85176219171,
      "time": 87,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8086445644"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "R2HTML",
      "role": "Imports"
    },
    {
      "package": "tcltk",
      "role": "Imports"
    },
    {
      "package": "tkrplot",
      "role": "Imports"
    },
    {
      "package": "xtable",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.89.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.88.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "gui",
    "geneexpression",
    "differentialexpression",
    "dataimport",
    "bayesian",
    "regression",
    "timecourse",
    "microarray",
    "mrnamicroarray",
    "twochannel",
    "batcheffect",
    "multiplecomparison",
    "normalization",
    "preprocessing",
    "qualitycontrol"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 21,
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/limmaGUI.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "AboutLimmaGUI",
    "AboutNormalization",
    "BChelp",
    "ChooseContrastsParameterization",
    "chooseDir",
    "ChooseEbayesStatistic",
    "ChooseParameterization",
    "ChoosePlotSymbolByClicking",
    "ChooseSpotType",
    "ComputeContrasts",
    "ComputeLinearModelFit",
    "CopyGraph",
    "CreateNewParameterization",
    "CreateTreeAndList",
    "DeleteContrastsParameterization",
    "deleteItemFromList",
    "DeleteParameterization",
    "DupCorBoxPlot",
    "ebayesBoxPlots",
    "evalRcode",
    "ExportAvalues",
    "ExportHTMLreport",
    "ExportMvalues",
    "ExportTopTable",
    "fixSeps",
    "GetBackgroundCorrectionMethod",
    "GetBetweenArrayNormalizationMethod",
    "GetCoef",
    "GetComponentsToExportInHTMLreport",
    "GetContrastsParameterizationName",
    "GetContrastsParameterizationNames",
    "GetDEcutoff",
    "GetDesignOrContrasts",
    "GetGeneLabelsOptions",
    "GetGenePixFlagWeightings",
    "GetImageAnalysisColumnHeadings",
    "GetImageProcessingFileType",
    "GetJpegOrPngParams",
    "GetJpegOrPngX11Params",
    "GetlimmaDataSetName",
    "GetlmFitMethod",
    "GetLowessType",
    "GetNEWxlim",
    "GetNormexpOffsetValue",
    "GetNumParametersNoTargets",
    "getPackageVersion",
    "GetParameterizationName",
    "GetParameterNames",
    "GetParametersAndOrContrasts",
    "GetPlotLabels",
    "GetPlotSize",
    "GetPlotTitle",
    "GetPValueCutoff",
    "GetReducedDuplicateSpacing",
    "GetRNATypesFrom.ContrastsFromDropDowns.String",
    "GetSlideNum",
    "GetSpotTypesForLinearModel",
    "GetSpotTypesIncludedNames",
    "GetWithinArrayNormalizationMethod",
    "GetWtAreaParams",
    "HeatDiagramDialog",
    "HeatDiagramPlot",
    "HowManyDups",
    "HTMLplotUsingFunction",
    "ImageArrayPlot",
    "ImageArrayPlotDialog",
    "imageplotlimmaGUI",
    "ImportMA",
    "ImportMADialog",
    "initGlobals",
    "InitNewParameterization",
    "LGchangeLog",
    "limmaGUI",
    "limmaGUIhelp",
    "limmaHelp",
    "lmFitMethodHelp",
    "LogOddsPlot",
    "MAPlot",
    "MAPlotAvg",
    "MBoxPlot",
    "MMPlot",
    "NewLimmaFile",
    "NormalizeNow",
    "nstrstr",
    "onDestroy",
    "onExit",
    "OpenALimmaFile",
    "OpenGALandTargetsandSpotTypesfiles",
    "OpenGALFile",
    "OpenLimmaFile",
    "OpenSpotTypesFile",
    "OpenTargetsFile",
    "plotMAColorCoded",
    "PlotOptions",
    "PrintTipGroupMAPlot",
    "QQTplot",
    "read.marrayTools",
    "ReadImageProcessingFiles",
    "Require",
    "Resize",
    "SaveAsLimmaFile",
    "SaveGraphAsJpeg",
    "SaveGraphAsPDF",
    "SaveGraphAsPNG",
    "SaveGraphAsPostscript",
    "SaveLimmaFile",
    "SelectPlotSymbols",
    "SetLayoutParameters",
    "SetupPlotKeyBindings",
    "SetupPlotMenus",
    "SetWD",
    "showChangeLog",
    "showCitations",
    "showGAL",
    "showTopTable",
    "SimplifyContrastsExpression",
    "strstr",
    "tclArrayVar",
    "TclRequire",
    "Try",
    "TryReadImgProcFile",
    "UpdateSpotTypesStatus",
    "UpDownOrBoth",
    "vennDiagramlimmaGUI",
    "VennDiagramPlot",
    "ViewDesignOrContrastsMatrixAsPairs",
    "ViewDesignOrContrastsMatrixInTable",
    "ViewExistingContrastsParameterization",
    "ViewExistingParameterization",
    "ViewRNATargets",
    "ViewSpotTypes",
    "WithinBetweenOrBoth",
    "wtflags2"
  ],
  "_help": [
    {
      "page": "LGchangelog",
      "title": "LimmaGUI Change Log",
      "topics": [
        "LGchangeLog"
      ]
    },
    {
      "page": "limmaGUI",
      "title": "Graphical User Interface for the limma microarray package",
      "topics": [
        "AboutLimmaGUI",
        "AboutNormalization",
        "BChelp",
        "ChooseContrastsParameterization",
        "chooseDir",
        "ChooseEbayesStatistic",
        "ChooseParameterization",
        "ChoosePlotSymbolByClicking",
        "ChooseSpotType",
        "ComputeContrasts",
        "ComputeLinearModelFit",
        "CopyGraph",
        "CreateNewParameterization",
        "CreateTreeAndList",
        "DeleteContrastsParameterization",
        "deleteItemFromList",
        "DeleteParameterization",
        "DupCorBoxPlot",
        "ebayesBoxPlots",
        "evalRcode",
        "ExportAvalues",
        "ExportHTMLreport",
        "ExportMvalues",
        "ExportTopTable",
        "fixSeps",
        "GetBackgroundCorrectionMethod",
        "GetBetweenArrayNormalizationMethod",
        "GetCoef",
        "GetComponentsToExportInHTMLreport",
        "GetContrastsParameterizationName",
        "GetContrastsParameterizationNames",
        "GetDEcutoff",
        "GetDesignOrContrasts",
        "GetGeneLabelsOptions",
        "GetGenePixFlagWeightings",
        "GetImageAnalysisColumnHeadings",
        "GetImageProcessingFileType",
        "GetJpegOrPngParams",
        "GetJpegOrPngX11Params",
        "GetlimmaDataSetName",
        "GetlmFitMethod",
        "GetLowessType",
        "GetNEWxlim",
        "GetNormexpOffsetValue",
        "GetNumParametersNoTargets",
        "getPackageVersion",
        "GetParameterizationName",
        "GetParameterNames",
        "GetParametersAndOrContrasts",
        "GetPlotLabels",
        "GetPlotSize",
        "GetPlotTitle",
        "GetPValueCutoff",
        "GetReducedDuplicateSpacing",
        "GetRNATypesFrom.ContrastsFromDropDowns.String",
        "GetSlideNum",
        "GetSpotTypesForLinearModel",
        "GetSpotTypesIncludedNames",
        "GetWithinArrayNormalizationMethod",
        "GetWtAreaParams",
        "HeatDiagramDialog",
        "HeatDiagramPlot",
        "HowManyDups",
        "HTMLplotUsingFunction",
        "ImageArrayPlot",
        "ImageArrayPlotDialog",
        "imageplotlimmaGUI",
        "ImportMA",
        "ImportMADialog",
        "initGlobals",
        "InitNewParameterization",
        "limmaGUI",
        "limmaGUIhelp",
        "limmaHelp",
        "lmFitMethodHelp",
        "LogOddsPlot",
        "MAPlot",
        "MAPlotAvg",
        "MBoxPlot",
        "MMPlot",
        "NewLimmaFile",
        "NormalizeNow",
        "nstrstr",
        "onDestroy",
        "onExit",
        "OpenALimmaFile",
        "OpenGALandTargetsandSpotTypesfiles",
        "OpenGALFile",
        "OpenLimmaFile",
        "OpenSpotTypesFile",
        "OpenTargetsFile",
        "plotMAColorCoded",
        "PlotOptions",
        "PrintTipGroupMAPlot",
        "QQTplot",
        "read.marrayTools",
        "readGALlimmaGUI",
        "ReadImageProcessingFiles",
        "Require",
        "Resize",
        "SaveAsLimmaFile",
        "SaveGraphAsJpeg",
        "SaveGraphAsPDF",
        "SaveGraphAsPNG",
        "SaveGraphAsPostscript",
        "SaveLimmaFile",
        "SelectPlotSymbols",
        "SetLayoutParameters",
        "SetupPlotKeyBindings",
        "SetupPlotMenus",
        "SetWD",
        "showChangeLog",
        "showCitations",
        "showGAL",
        "showTopTable",
        "SimplifyContrastsExpression",
        "strstr",
        "tclArrayVar",
        "TclRequire",
        "Try",
        "TryReadImgProcFile",
        "UpdateSpotTypesStatus",
        "UpDownOrBoth",
        "vennDiagramlimmaGUI",
        "VennDiagramPlot",
        "ViewDesignOrContrastsMatrixAsPairs",
        "ViewDesignOrContrastsMatrixInTable",
        "ViewExistingContrastsParameterization",
        "ViewExistingParameterization",
        "ViewRNATargets",
        "ViewSpotTypes",
        "WithinBetweenOrBoth",
        "wtflags2"
      ]
    }
  ],
  "_rundeps": [
    "limma",
    "R2HTML",
    "statmod",
    "tkrplot",
    "xtable"
  ],
  "_vignettes": [
    {
      "source": "extract.Rnw",
      "filename": "extract.pdf",
      "title": "Extracting limma objects from limmaGUI files",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 19:51:24",
      "modified": "2013-11-01 19:51:24",
      "commits": 1
    },
    {
      "source": "limmaGUI.Rnw",
      "filename": "limmaGUI.pdf",
      "title": "limmaGUI Vignette",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 19:51:24",
      "modified": "2013-11-01 19:51:24",
      "commits": 1
    }
  ],
  "_score": 4.6020599913279625,
  "_indexed": true,
  "_nocasepkg": "limmagui",
  "_universes": [
    "bioc",
    "gksmyth"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.89.0",
      "date": "2026-07-04T23:40:16.000Z",
      "distro": "resolute",
      "commit": "d80f056590f52caaf5aa59b032e5bd2a7a986297",
      "fileid": "https://r2.ropensci.org/c3711de02af2ff6d6b92303c4530ba3147a19bd6f9f72b5c53736acd1fa28e8e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723204780"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.89.0",
      "date": "2026-07-04T23:41:08.000Z",
      "distro": "resolute",
      "commit": "d80f056590f52caaf5aa59b032e5bd2a7a986297",
      "fileid": "https://r2.ropensci.org/67221fa4077b3fe5e48d1533cbb4f45008af1f393c4c2c59bdfcba134235109b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723204780"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.89.0",
      "date": "2026-07-04T23:39:22.000Z",
      "commit": "d80f056590f52caaf5aa59b032e5bd2a7a986297",
      "fileid": "https://r2.ropensci.org/93e331b6d76334dcdfb8b61d4c15b5c3150b69e2b5df2b0a3aecf37e5a8386d5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723204780"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.89.0",
      "date": "2026-07-04T23:39:27.000Z",
      "commit": "d80f056590f52caaf5aa59b032e5bd2a7a986297",
      "fileid": "https://r2.ropensci.org/d384f8d9f1dca5bfa78b9295008a5275b4dda9d4a2316a17dd96d52ce37aa040",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723204780"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.89.0",
      "date": "2026-07-04T23:39:09.000Z",
      "commit": "d80f056590f52caaf5aa59b032e5bd2a7a986297",
      "fileid": "https://r2.ropensci.org/56584bedb92b53809a32643e10a86ff272334ec4f7e787bd0ba1007428eead05",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723204780"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.89.0",
      "date": "2026-07-04T23:39:04.000Z",
      "commit": "d80f056590f52caaf5aa59b032e5bd2a7a986297",
      "fileid": "https://r2.ropensci.org/268135a63941cc9d77a953e2afe92a4a6ac2e1de9410302dd3f0e60db2bcf26d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723204780"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.89.0",
      "date": "2026-07-04T23:39:07.000Z",
      "commit": "d80f056590f52caaf5aa59b032e5bd2a7a986297",
      "fileid": "https://r2.ropensci.org/94ee6c5df06bfe6f8027bbc15ea716292afb9cde21ea9d0f3afa436fdfcea8c6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723204780"
    }
  ]
}