# iSEE extension for panels related to differential expression analysis

## Documentation for package ‘iSEEde’ version 1.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.cacheCommonInfo-method | The DETable class
.cacheCommonInfo-method | The LogFCLogFCPlot class
.cacheCommonInfo-method | The MAPlot class
.cacheCommonInfo-method | The VolcanoPlot class
.createObservers-method | The DETable class
.createObservers-method | The LogFCLogFCPlot class
.createObservers-method | The MAPlot class
.createObservers-method | The VolcanoPlot class
.defineDataInterface-method | The DETable class
.defineDataInterface-method | The LogFCLogFCPlot class
.defineDataInterface-method | The MAPlot class
.defineDataInterface-method | The VolcanoPlot class
.fullName-method | The DETable class
.fullName-method | The LogFCLogFCPlot class
.fullName-method | The MAPlot class
.fullName-method | The VolcanoPlot class
.generateDotPlotData-method | The LogFCLogFCPlot class
.generateDotPlotData-method | The MAPlot class
.generateDotPlotData-method | The VolcanoPlot class
.generateTable-method | The DETable class
.panelColor-method | The DETable class
.panelColor-method | The LogFCLogFCPlot class
.panelColor-method | The MAPlot class
.panelColor-method | The VolcanoPlot class
.refineParameters-method | The DETable class
.refineParameters-method | The LogFCLogFCPlot class
.refineParameters-method | The MAPlot class
.refineParameters-method | The VolcanoPlot class
averageLog2 | Generics for Differential Expression Results
averageLog2-method | The iSEEDESeq2Results class
averageLog2-method | The iSEELimmaResults class
averageLog2-method | The iSEEedgeRResults class
contrastResults | Extract contrast results embedded in a SummarizedExperiment object
contrastResultsNames | Extract contrast results embedded in a SummarizedExperiment object
de-generics | Generics for Differential Expression Results
DETable | The DETable class
DETable-class | The DETable class
embedContrastResults | Generics for Embbedding Results into a SummarizedExperiment Object
embedContrastResults-method | The iSEEDESeq2Results class
embedContrastResults-method | The iSEELimmaResults class
embedContrastResults-method | The iSEEedgeRResults class
embedContrastResults-method | Generics for Embbedding Results into a SummarizedExperiment Object
embedContrastResultsMethods | Generics for Embbedding Results into a SummarizedExperiment Object
initialize-method | The DETable class
initialize-method | The LogFCLogFCPlot class
initialize-method | The MAPlot class
initialize-method | The VolcanoPlot class
iSEEDESeq2Results | The iSEEDESeq2Results class
iSEEDESeq2Results-class | The iSEEDESeq2Results class
iSEEedgeRResults | The iSEEedgeRResults class
iSEEedgeRResults-class | The iSEEedgeRResults class
iSEELimmaResults | The iSEELimmaResults class
iSEELimmaResults-class | The iSEELimmaResults class
log2FoldChange | Generics for Differential Expression Results
log2FoldChange-method | The iSEEDESeq2Results class
log2FoldChange-method | The iSEELimmaResults class
log2FoldChange-method | The iSEEedgeRResults class
LogFCLogFCPlot | The LogFCLogFCPlot class
LogFCLogFCPlot-class | The LogFCLogFCPlot class
MAPlot | The MAPlot class
MAPlot-class | The MAPlot class
pValue | Generics for Differential Expression Results
pValue-method | The iSEEDESeq2Results class
pValue-method | The iSEELimmaResults class
pValue-method | The iSEEedgeRResults class
showAsCell-method | The iSEEDESeq2Results class
showAsCell-method | The iSEELimmaResults class
showAsCell-method | The iSEEedgeRResults class
utils-SummarizedExperiment | Generics for Embbedding Results into a SummarizedExperiment Object
VolcanoPlot | The VolcanoPlot class
VolcanoPlot-class | The VolcanoPlot class