Package: affylmGUI 1.81.0

Gordon Smyth

affylmGUI: GUI for limma Package with Affymetrix Microarrays

A Graphical User Interface (GUI) for analysis of Affymetrix microarray gene expression data using the affy and limma packages.

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

affylmGUI_1.81.0.tar.gz
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affylmGUI_1.81.0.tgz(r-4.4-any)affylmGUI_1.81.0.tgz(r-4.3-any)
affylmGUI_1.81.0.tar.gz(r-4.5-noble)affylmGUI_1.81.0.tar.gz(r-4.4-noble)
affylmGUI.pdf |affylmGUI.html✨
affylmGUI/json (API)
NEWS

# Install 'affylmGUI' in R:

install.packages('affylmGUI', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:affylmGUI-1.79.0(bioc 3.20)affylmGUI-1.78.0(bioc 3.19)

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

gui geneexpression transcription differentialexpression dataimport bayesian regression timecourse microarray mrnamicroarray onechannel proprietaryplatforms batcheffect multiplecomparison normalization preprocessing qualitycontrol

3.60 score 3 scripts 442 downloads 104 exports 49 dependencies

Last updated 26 days agofrom:cc3b06c8f7. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 30 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 30 2024
R-4.4-mac	NOTE	Oct 30 2024
R-4.3-win	NOTE	Oct 30 2024
R-4.3-mac	NOTE	Oct 30 2024

Exports:AboutaffylmGUI affyHelp affylmGUI 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 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

Dependencies:affy affyio affyPLM AnnotationDbi askpass Biobase BiocGenerics BiocManager Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI fastmap gcrma GenomeInfoDb GenomeInfoDbData glue httr IRanges jsonlite KEGGREST lifecycle limma memoise mime openssl pkgconfig plogr png preprocessCore R2HTML R6 rlang RSQLite S4Vectors statmod sys tkrplot UCSC.utils vctrs xtable XVector zlibbioc

affylmGUI Vignette

Rendered fromaffylmGUI.Rnwusingutils::Sweaveon Oct 30 2024.

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

Extracting affy and limma objects from affylmGUI files

Rendered fromextract.Rnwusingutils::Sweaveon Oct 30 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The affylmGUI Package: Graphical User Interface for limma analysis of Affymetrix microarrays	affylmGUI-package
Graphical User Interface for the limma microarray package	affylmGUI
Internal Functions	AboutaffylmGUI 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 initGlobals IntensityHistogram IntensityHistogramAll internal 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