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() `alphaThreshold<-`()

Alpha threshold

apeglmResults()

Run a quick pairwise contrast using lfcShrink with apeglm

as

Force an object to belong to a class

baseMeanThreshold() `baseMeanThreshold<-`()

Base mean threshold

combine()

Combine multiple objects

contrastName() `contrastName<-`()

Contrast name

contrastSamples()

Samples corresponding to a differential expression contrast

correlation()

Correlation

dds_list

List of DESeqDataSet example objects

deg()

Differentially expressed genes

degIntersection()

Intersection of differentially expressed genes

degPerContrast()

Base mean threshold

deseq

DESeq2 example analysis

export()

Export

`[`(<DESeqAnalysis>,<ANY>,<ANY>,<ANY>)

Extract or replace parts of an object

importPairwiseContrasts()

Import pairwise contrasts from a file

interestingGroups() `interestingGroups<-`()

Interesting groups

lfcShrink() `lfcShrink<-`()

Shrink log2 fold changes

lfcShrinkType()

Shrunken log2 fold change (LFC) type

lfcThreshold() `lfcThreshold<-`()

Log2 fold change threshold

matchMetadataToFiles()

Match user metadata to file names used for tximport

plotBaseMean()

Plot base mean distribution

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

plotHeatmap() plotCorrelationHeatmap() plotQuantileHeatmap()

Heatmap

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