DESeqAnalysis           DESeq2 differential expression analysis
DESeqAnalysis-class     DESeq2 differential expression analysis
DESeqAnalysisList       List containing related DESeq2 analyses
DESeqAnalysisList-class
                        List containing related DESeq2 analyses
alphaSummary            Alpha level cutoff summary statistics
as                      Force an object to belong to a class
contrastName            Contrast name
contrastSamples         Samples corresponding to a differential
                        expression contrast
deg                     Differentially expressed genes
deseq                   DESeq2 example analysis
export                  Export
importPairwiseContrasts
                        Import pairwise contrasts from a file
lfcShrinkType           Shrunken log2 fold change (LFC) type
markdown                Markdown
plotBaseMean            Plot base mean distribution
plotCounts              Plot counts
plotDEGHeatmap          Differentially expressed gene heatmap
plotDEGPCA              Plot differentially expressed gene principal
                        component analysis
plotDEGUpset            UpSet plot of directional DEG intersections
                        across contrasts
plotMA                  MA-plot: plot differences versus averages for
                        high-throughput data
plotPCA                 Principal component analysis plot
plotVolcano             Volcano plot
results                 Results
resultsMatrix           DESeqResults matrix
resultsNames            Results names
resultsTables           Results tables
sampleData              Sample data
show                    Show an object
topTables               Top tables
transformType           Variance-stabilizing transformation type
updateObject            Update an object to its current class
                        definition
