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All functions

DESeqAnalysis-class
DESeq2 differential expression analysis
DESeqAnalysis()
DESeq2 differential expression analysis
DESeqAnalysisList-class
List containing related DESeq2 analyses
DESeqAnalysisList()
List containing related DESeq2 analyses
DESeqResultsList-class
List containing related DESeqResults objects
DESeqResultsList()
List containing related DESeqResults objects
alphaSummary()
Alpha level cutoff summary statistics
alphaThreshold
Alpha threshold
apeglmResults()
Run a quick pairwise contrast using lfcShrink with apeglm
baseMeanThreshold
Base mean threshold
as.DESeqDataSet() as.DESeqTransform()
Coercion methods
combine()
Combine multiple objects
contrastName() `contrastName<-`()
Contrast name
contrastSamples()
Samples corresponding to a differential expression contrast
correlation()
Correlation
deg()
Differentially expressed genes
degIntersection()
Intersection of differentially expressed genes
degPerContrast()
Base mean threshold
deseq
DESeq2 example analysis
deseqMinimal
Minimal DESeq2 example analysis
export()
Export
`[`(<DESeqAnalysis>,<ANY>,<ANY>,<ANY>)
Extract or replace parts of an object
importPairwiseContrasts()
Import pairwise contrasts from a file
interestingGroups
Interesting groups
lfcShrink() `lfcShrink<-`()
Shrink log2 fold changes
lfcShrinkType()
Shrunken log2 fold change (LFC) type
lfcThreshold
Log2 fold change threshold
matchMetadataToFiles()
Match user metadata to file names used for tximport
plotBaseMean()
Plot base mean distribution
plotContrastScatter()
Plot scatterplot of differential expression contrast
plotCounts()
Plot counts
plotDEGHeatmap()
Differentially expressed gene heatmap
plotDEGPCA()
Plot differentially expressed gene principal component analysis
plotDEGStackedBar()
Stacked bar plot of DEGs
plotDEGUpset()
UpSet plot of directional DEG intersections across contrasts
plotCorrelationHeatmap() plotHeatmap() plotQuantileHeatmap()
Heatmap
plotLFC()
Plot log2 fold change distributions
plotMA()
MA plot
plotPCA()
Principal component analysis plot
plotVolcano()
Volcano plot
prepareTximportFiles()
Prepare quant files for tximport
results()
Results
resultsDiff()
Relative difference of results
resultsMatrix()
DESeq aggregate results matrix
resultsNames() `resultsNames<-`()
Results names
resultsTables()
Results tables
sampleData()
Sample data
show()
Show an object
topTables()
Top tables
transformType()
Variance-stabilizing transformation type
updateObject()
Update object