# Inference of differential exon usage in RNA-Seq

## Documentation for package ‘DEXSeq’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

$<--method | Subset and replacements of DEXSeqDataSet slots
colData<--method | Subset and replacements of DEXSeqDataSet slots
counts | Accessors for the 'counts' slot of a DEXSeqResults object.
counts-method | Accessors for the 'counts' slot of a DEXSeqResults object.
DEXSeq | Performs the differential exon usage test in a single command
DEXSeq-defunct | This functions are deprecated and will become defunct.
DEXSeqDataSet | DEXSeqDataSet object and constructors
DEXSeqDataSet-class | DEXSeqDataSet object and constructors
DEXSeqDataSetFromHTSeq | DEXSeqDataSet object and constructors
DEXSeqDataSetFromSE | DEXSeqDataSet object and constructors
DEXSeqHTML | DEXSeq HTML report writer
DEXSeqResults | DEXSeqResults object
DEXSeqResults-class | DEXSeqResults object
estimateDispersions | Estimate the dispersions for a DEXSeqDataSet
estimateDispersions-method | Estimate the dispersions for a DEXSeqDataSet
estimateExonFoldChanges | Estimates exon usage coefficients from the fitted terms of the GLM.
estimateSizeFactors | Estimate the size factors for a DEXSeqDataSet
estimateSizeFactors-method | Estimate the size factors for a DEXSeqDataSet
exonIDs | Accessor functions for DEXSeqDataSet details
exonIDs<- | Accessor functions for DEXSeqDataSet details
featureCounts | Accessor functions for DEXSeqDataSet details
featureIDs | Accessor functions for DEXSeqDataSet details
featureIDs<- | Accessor functions for DEXSeqDataSet details
findOverlaps | Methods from GRanges overlaps for the DEXSeq object
findOverlaps-method | Methods from GRanges overlaps for the DEXSeq object
findOverlaps-methods | Methods from GRanges overlaps for the DEXSeq object
geneIDs | Accessor functions for DEXSeqDataSet details
geneIDs<- | Accessor functions for DEXSeqDataSet details
groupIDs | Accessor functions for DEXSeqDataSet details
groupIDs<- | Accessor functions for DEXSeqDataSet details
perGeneQValue | Summarize per-exon p-values into per-gene q-values.
plotDEXSeq | Visualization of the per gene DEXSeq results.
plotDispEsts | Plot dispersion estimates
plotDispEsts-method | Plot dispersion estimates
plotMA | Generate an MA plot
plotMA-method | Generate an MA plot
plotMA-methods | Generate an MA plot
sampleAnnotation | Accessor functions for DEXSeqDataSet details
subsetByOverlaps | Methods from GRanges overlaps for the DEXSeq object
subsetByOverlaps-method | Methods from GRanges overlaps for the DEXSeq object
subsetByOverlaps-methods | Methods from GRanges overlaps for the DEXSeq object
testForDEU | Test for Differential Exon Usage.
[-method | Subset and replacements of DEXSeqDataSet slots