{
  "_id": "6a19eb481d7bb097a09c7174",
  "Package": "affylmGUI",
  "Version": "1.87.0",
  "Date": "2020-04-13",
  "Title": "GUI for limma Package with Affymetrix Microarrays",
  "Author": "James Wettenhall [cre,aut], Gordon Smyth [aut], Ken Simpson\n[aut], Keith Satterley [ctb]",
  "Maintainer": "Gordon Smyth <smyth@wehi.edu.au>",
  "Description": "A Graphical User Interface (GUI) for analysis of\nAffymetrix microarray gene expression data using the affy and\nlimma packages.",
  "License": "GPL (>=2)",
  "URL": "http://bioinf.wehi.edu.au/affylmGUI/",
  "biocViews": "GUI, GeneExpression, Transcription, DifferentialExpression,\nDataImport, Bayesian, Regression, TimeCourse, Microarray,\nmRNAMicroarray, OneChannel, ProprietaryPlatforms, BatchEffect,\nMultipleComparison, Normalization, Preprocessing,\nQualityControl",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:30:33 UTC",
  "RemoteUrl": "https://github.com/bioc/affylmGUI",
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    "User": "root"
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    "geneexpression",
    "transcription",
    "differentialexpression",
    "dataimport",
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    "regression",
    "timecourse",
    "microarray",
    "mrnamicroarray",
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    "name": "Bioconductor",
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    "extra/citation.html",
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    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
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  "_cranurl": false,
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    "affyHelp",
    "affylmGUI",
    "affylmGUIhelp",
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    "affyPlotMAcontrast",
    "ChooseCDF",
    "ChooseContrastParameterization",
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    "ChooseEbayesStatistic",
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    "ComputeLinearModelFit",
    "CopyGraph",
    "DeleteContrastParameterization",
    "DensityPlot",
    "DensityPlotAll",
    "evalRcode",
    "ExportHTMLreport",
    "ExportNormalizedExpressionValues",
    "ExportTopTable",
    "fixSeps",
    "generalPlotFunction",
    "GetComponentsToExportInHTMLreport",
    "GetContrast",
    "GetContrastNamesForHeatDiagram",
    "GetContrastParameterizationName",
    "GetContrasts",
    "GetDEcutoff",
    "GetGeneLabelsOptions",
    "GetJpegOrPngParams",
    "GetJpegOrPngX11Params",
    "GetlimmaDataSetName",
    "GetLogPLMDataChoice",
    "GetMultipleContrasts",
    "GetNormalizationMethod",
    "getPackageVersion",
    "GetParameterizationName",
    "GetPlotLabels",
    "GetPlotSize",
    "GetPlotTitle",
    "GetPValueCutoff",
    "GetResidualTypeChoice",
    "GetRNATypesFrom.ContrastsFromDropDowns.String",
    "GetSetNames",
    "GetSlideNum",
    "GetSlideNums",
    "GetWhichProbes",
    "GetWtAreaParams",
    "GetWtFlagParams",
    "HeatDiagramDialog",
    "HeatDiagramPlot",
    "HTMLplotUsingFunction",
    "ImageArrayPlot",
    "ImageQualityResidualPlot",
    "ImageQualityWeightPlot",
    "initGlobals",
    "IntensityHistogram",
    "IntensityHistogramAll",
    "limmaHelp",
    "LogOddsPlot",
    "NewLimmaFile",
    "NormalizedIntensityBoxPlot",
    "NormalizeNow",
    "nstrstr",
    "NUSEPlotAll",
    "onDestroy",
    "onExit",
    "OpenALimmaFile",
    "OpenCDFandTargetsfiles",
    "OpenCDFFile",
    "OpenLimmaFile",
    "OpenTargetsFile",
    "PlotOptions",
    "QQTplot",
    "RawIntensityBoxPlot",
    "Require",
    "Resize",
    "RLEPlotAll",
    "RNADegradationPlotAll",
    "SaveAsLimmaFile",
    "SaveGraphAsJpeg",
    "SaveGraphAsPDF",
    "SaveGraphAsPNG",
    "SaveGraphAsPostscript",
    "SaveLimmaFile",
    "SetupPlotKeyBindings",
    "SetupPlotMenus",
    "SetWD",
    "showChangeLog",
    "showCitations",
    "showTopTable",
    "SimplifyContrastsExpression",
    "strstr",
    "tclArrayVar",
    "TclRequire",
    "Try",
    "TryReadImgProcFile",
    "UpDownOrBoth",
    "vennDiagramaffylmGUI",
    "VennDiagramPlot",
    "ViewContrastsMatrixAsPairs",
    "ViewContrastsMatrixInTable",
    "ViewExistingContrastParameterization",
    "ViewRNATargets"
  ],
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      "page": "affylmGU-package",
      "title": "The affylmGUI Package: Graphical User Interface for limma analysis of Affymetrix microarrays",
      "topics": [
        "affylmGUI-package"
      ]
    },
    {
      "page": "affylmGUI",
      "title": "Graphical User Interface for the limma microarray package",
      "topics": [
        "affylmGUI"
      ]
    },
    {
      "page": "internal",
      "title": "Internal Functions",
      "topics": [
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        "affyHelp",
        "affylmGUIhelp",
        "affyPlotMA",
        "affyPlotMAcontrast",
        "ChooseCDF",
        "ChooseContrastParameterization",
        "chooseDir",
        "ChooseEbayesStatistic",
        "ComputeContrasts",
        "ComputeLinearModelFit",
        "CopyGraph",
        "DeleteContrastParameterization",
        "DensityPlot",
        "DensityPlotAll",
        "evalRcode",
        "ExportHTMLreport",
        "ExportNormalizedExpressionValues",
        "ExportTopTable",
        "fixSeps",
        "generalPlotFunction",
        "GetComponentsToExportInHTMLreport",
        "GetContrast",
        "GetContrastNamesForHeatDiagram",
        "GetContrastParameterizationName",
        "GetContrasts",
        "GetDEcutoff",
        "GetGeneLabelsOptions",
        "GetJpegOrPngParams",
        "GetJpegOrPngX11Params",
        "GetlimmaDataSetName",
        "GetLogPLMDataChoice",
        "GetMultipleContrasts",
        "GetNormalizationMethod",
        "getPackageVersion",
        "GetParameterizationName",
        "GetPlotLabels",
        "GetPlotSize",
        "GetPlotTitle",
        "GetPValueCutoff",
        "GetResidualTypeChoice",
        "GetRNATypesFrom.ContrastsFromDropDowns.String",
        "GetSetNames",
        "GetSlideNum",
        "GetSlideNums",
        "GetWhichProbes",
        "GetWtAreaParams",
        "GetWtFlagParams",
        "HeatDiagramDialog",
        "HeatDiagramPlot",
        "HTMLplotUsingFunction",
        "ImageArrayPlot",
        "ImageQualityResidualPlot",
        "ImageQualityWeightPlot",
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        "IntensityHistogramAll",
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        "limmaHelp",
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