Package: limmaGUI 1.83.0

Gordon Smyth

limmaGUI: GUI for limma Package With Two Color Microarrays

A Graphical User Interface for differential expression analysis of two-color microarray data using the limma package.

Authors:James Wettenhall [aut], Gordon Smyth [aut], Keith Satterley [ctb]

limmaGUI_1.83.0.tar.gz
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limmaGUI.pdf |limmaGUI.html✨
limmaGUI/json (API)

# Install 'limmaGUI' in R:
install.packages('limmaGUI', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:limmaGUI-1.81.0(bioc 3.20)limmaGUI-1.80.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

guigeneexpressiondifferentialexpressiondataimportbayesianregressiontimecoursemicroarraymrnamicroarraytwochannelbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrol

4.60 score 1 scripts 297 downloads 21 mentions 133 exports 5 dependencies

Last updated 23 days agofrom:39141a00bd. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:AboutLimmaGUIAboutNormalizationBChelpChooseContrastsParameterizationchooseDirChooseEbayesStatisticChooseParameterizationChoosePlotSymbolByClickingChooseSpotTypeComputeContrastsComputeLinearModelFitCopyGraphCreateNewParameterizationCreateTreeAndListDeleteContrastsParameterizationdeleteItemFromListDeleteParameterizationDupCorBoxPlotebayesBoxPlotsevalRcodeExportAvaluesExportHTMLreportExportMvaluesExportTopTablefixSepsGetBackgroundCorrectionMethodGetBetweenArrayNormalizationMethodGetCoefGetComponentsToExportInHTMLreportGetContrastsParameterizationNameGetContrastsParameterizationNamesGetDEcutoffGetDesignOrContrastsGetGeneLabelsOptionsGetGenePixFlagWeightingsGetImageAnalysisColumnHeadingsGetImageProcessingFileTypeGetJpegOrPngParamsGetJpegOrPngX11ParamsGetlimmaDataSetNameGetlmFitMethodGetLowessTypeGetNEWxlimGetNormexpOffsetValueGetNumParametersNoTargetsgetPackageVersionGetParameterizationNameGetParameterNamesGetParametersAndOrContrastsGetPlotLabelsGetPlotSizeGetPlotTitleGetPValueCutoffGetReducedDuplicateSpacingGetRNATypesFrom.ContrastsFromDropDowns.StringGetSlideNumGetSpotTypesForLinearModelGetSpotTypesIncludedNamesGetWithinArrayNormalizationMethodGetWtAreaParamsHeatDiagramDialogHeatDiagramPlotHowManyDupsHTMLplotUsingFunctionImageArrayPlotImageArrayPlotDialogimageplotlimmaGUIImportMAImportMADialoginitGlobalsInitNewParameterizationLGchangeLoglimmaGUIlimmaGUIhelplimmaHelplmFitMethodHelpLogOddsPlotMAPlotMAPlotAvgMBoxPlotMMPlotNewLimmaFileNormalizeNownstrstronDestroyonExitOpenALimmaFileOpenGALandTargetsandSpotTypesfilesOpenGALFileOpenLimmaFileOpenSpotTypesFileOpenTargetsFileplotMAColorCodedPlotOptionsPrintTipGroupMAPlotQQTplotread.marrayToolsReadImageProcessingFilesRequireResizeSaveAsLimmaFileSaveGraphAsJpegSaveGraphAsPDFSaveGraphAsPNGSaveGraphAsPostscriptSaveLimmaFileSelectPlotSymbolsSetLayoutParametersSetupPlotKeyBindingsSetupPlotMenusSetWDshowChangeLogshowCitationsshowGALshowTopTableSimplifyContrastsExpressionstrstrtclArrayVarTclRequireTryTryReadImgProcFileUpdateSpotTypesStatusUpDownOrBothvennDiagramlimmaGUIVennDiagramPlotViewDesignOrContrastsMatrixAsPairsViewDesignOrContrastsMatrixInTableViewExistingContrastsParameterizationViewExistingParameterizationViewRNATargetsViewSpotTypesWithinBetweenOrBothwtflags2

Dependencies:limmaR2HTMLstatmodtkrplotxtable

Extracting limma objects from limmaGUI files

Rendered fromextract.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2013-11-01
Started: 2013-11-01

limmaGUI Vignette

Rendered fromlimmaGUI.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2013-11-01
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
LimmaGUI Change LogLGchangeLog
Graphical User Interface for the limma microarray packageAboutLimmaGUI 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