API for acidgenomics/DESeqAnalysis
DESeq2 Analysis Utilities

Global functions
.addIsDECol Source code
.coerceResultsToList Source code
.contrast2coef Source code
.ddsMsg Source code
.exportResultsMatrices Source code
.exportResultsTables Source code
.joinCounts Source code
.joinRowData Source code
.transformCountsAxisLabel Source code
.whichResults Source code
DESeqAnalysis Man page
DESeqAnalysis-class Man page
DESeqAnalysisList Man page Source code
DESeqAnalysisList-class Man page
alphaSummary Man page
alphaSummary,DESeqDataSet-method Man page
apeglmContrast Man page Source code
apeglmResults Man page
apeglmResults,DESeqDataSet-method Man page
as Man page
coerce Man page
coerce,DESeqAnalysis,DESeqDataSet-method Man page
coerce,DESeqAnalysis,DESeqResults-method Man page
coerce,DESeqAnalysis,DESeqTransform-method Man page
contrastName Man page
contrastName,DESeqAnalysis-method Man page
contrastName,DESeqResults-method Man page
contrastName<- Man page
contrastName<-,DESeqResults,character-method Man page
contrastNames Man page
contrastNames,DESeqAnalysis-method Man page
contrastNames,DESeqDataSet-method Man page
contrastNames<- Man page
contrastNames<-,DESeqAnalysis,character-method Man page
contrastSamples Man page
contrastSamples,DESeqAnalysis-method Man page
correlation Man page
correlation,DESeqAnalysis,missingOrNULL-method Man page
correlation,DESeqResults,DESeqResults-method Man page
deg Man page
deg,DESeqAnalysis-method Man page
deg,DESeqResults-method Man page
deprecated Man page
deseq Man page
export Man page
export,DESeqAnalysis-method Man page
export,DESeqDataSet-method Man page
importPairwiseContrasts Man page Source code
lfcShrinkType Man page
lfcShrinkType,DESeqAnalysis-method Man page
lfcShrinkType,DESeqResults-method Man page
markdown Man page
markdown,DESeqAnalysis-method Man page
matchMetadataToFiles Man page Source code
params Man page
plotBaseMean Man page
plotBaseMean,DESeqAnalysis-method Man page
plotBaseMean,DESeqDataSet-method Man page
plotBaseMean,DESeqResults-method Man page
plotBaseMean,numeric-method Man page
plotCorrelationHeatmap Man page
plotCorrelationHeatmap,DESeqAnalysis-method Man page
plotCounts Man page
plotCounts,DESeqAnalysis-method Man page
plotCounts,DESeqDataSet-method Man page
plotCounts,DESeqTransform-method Man page
plotDEGHeatmap Man page
plotDEGHeatmap,DESeqAnalysis-method Man page
plotDEGHeatmap,DESeqResults-method Man page
plotDEGPCA Man page
plotDEGPCA,DESeqAnalysis-method Man page
plotDEGPCA,DESeqResults-method Man page
plotDEGUpset Man page
plotDEGUpset,DESeqAnalysis-method Man page
plotHeatmap Man page
plotHeatmap,DESeqAnalysis-method Man page
plotMA Man page
plotMA,DESeqAnalysis-method Man page
plotMA,DESeqResults-method Man page
plotMeanAverage Man page Source code
plotPCA Man page
plotPCA,DESeqAnalysis-method Man page
plotPCA,DESeqTransform-method Man page
plotQuantileHeatmap Man page
plotQuantileHeatmap,DESeqAnalysis-method Man page
plotVolcano Man page
plotVolcano,DESeqAnalysis-method Man page
plotVolcano,DESeqResults-method Man page
prepareTximportFiles Man page Source code
results Man page
results,DESeqAnalysis-method Man page
results,DESeqDataSet-method Man page
resultsMatrix Man page
resultsMatrix,DESeqAnalysis-method Man page
resultsMatrix,DESeqAnalysisList-method Man page
resultsNames Man page
resultsNames,DESeqAnalysis-method Man page
resultsNames,DESeqDataSet-method Man page
resultsNames<- Man page
resultsNames<-,DESeqAnalysis,character-method Man page
resultsTables Man page
resultsTables,DESeqAnalysis-method Man page
resultsTables,DESeqResults-method Man page
sampleData Man page
sampleData,DESeqAnalysis-method Man page
show Man page
show,DESeqAnalysis-method Man page
topTables Man page
topTables,DESeqAnalysis-method Man page
topTables,DESeqResults-method Man page
topTables,list-method Man page
transformType Man page
transformType,DESeqAnalysis-method Man page
transformType,DESeqTransform-method Man page
updateObject Man page
updateObject,DESeqAnalysis-method Man page
acidgenomics/DESeqAnalysis documentation built on Nov. 21, 2019, 3:56 p.m.