# DESeq2 Analysis Utilities

## Documentation for package ‘DESeqAnalysis’ version 0.2.13

- DESCRIPTION file.

## Help Pages

alphaSummary | Alpha level cutoff summary statistics
alphaSummary-method | Alpha level cutoff summary statistics
apeglmResults | Run a quick pairwise contrast using lfcShrink with apeglm
apeglmResults-method | Run a quick pairwise contrast using lfcShrink with apeglm
as | Force an object to belong to a class
coerce | Force an object to belong to a class
coerce-method | Force an object to belong to a class
contrastName | Contrast name
contrastName-method | Contrast name
contrastName<- | Contrast name
contrastName<--method | Contrast name
contrastNames | Results names
contrastNames-method | Results names
contrastNames<- | Results names
contrastNames<--method | Results names
contrastSamples | Samples corresponding to a differential expression contrast
contrastSamples-method | Samples corresponding to a differential expression contrast
correlation | Correlation
correlation-method | Correlation
deg | Differentially expressed genes
deg-method | Differentially expressed genes
deseq | DESeq2 example analysis
DESeqAnalysis | DESeq2 differential expression analysis
DESeqAnalysis-class | DESeq2 differential expression analysis
DESeqAnalysisList | List containing related DESeq2 analyses
DESeqAnalysisList-class | List containing related DESeq2 analyses
export | Export
export-method | Export
importPairwiseContrasts | Import pairwise contrasts from a file
lfcShrinkType | Shrunken log2 fold change (LFC) type
lfcShrinkType-method | Shrunken log2 fold change (LFC) type
markdown | Markdown
markdown-method | Markdown
matchMetadataToFiles | Match user metadata to file names used for tximport
plotBaseMean | Plot base mean distribution
plotBaseMean-method | Plot base mean distribution
plotCorrelationHeatmap | Heatmap
plotCorrelationHeatmap-method | Heatmap
plotCounts | Plot counts
plotCounts-method | Plot counts
plotDEGHeatmap | Differentially expressed gene heatmap
plotDEGHeatmap-method | Differentially expressed gene heatmap
plotDEGPCA | Plot differentially expressed gene principal component analysis
plotDEGPCA-method | Plot differentially expressed gene principal component analysis
plotDEGUpset | UpSet plot of directional DEG intersections across contrasts
plotDEGUpset-method | UpSet plot of directional DEG intersections across contrasts
plotHeatmap | Heatmap
plotHeatmap-method | Heatmap
plotMA | MA-plot: plot differences versus averages for high-throughput data
plotMA-method | MA-plot: plot differences versus averages for high-throughput data
plotMeanAverage | MA-plot: plot differences versus averages for high-throughput data
plotPCA | Principal component analysis plot
plotPCA-method | Principal component analysis plot
plotQuantileHeatmap | Heatmap
plotQuantileHeatmap-method | Heatmap
plotVolcano | Volcano plot
plotVolcano-method | Volcano plot
prepareTximportFiles | Prepare quant files for tximport
results | Results
results-method | Results
resultsMatrix | DESeq aggregate results matrix
resultsMatrix-method | DESeq aggregate results matrix
resultsNames | Results names
resultsNames-method | Results names
resultsNames<- | Results names
resultsNames<--method | Results names
resultsTables | Results tables
resultsTables-method | Results tables
sampleData | Sample data
sampleData-method | Sample data
show | Show an object
show-method | Show an object
topTables | Top tables
topTables-method | Top tables
transformType | Variance-stabilizing transformation type
transformType-method | Variance-stabilizing transformation type
updateObject | Update an object to its current class definition
updateObject-method | Update an object to its current class definition