DEUresultTable          Get a result table from the analysis workflow.
DEXSeq-deprecated       This functions are deprecated and will become
                        defunct.
DEXSeqHTML              HTML report writer
ExonCountSet            "ExonCountSet", a container for exon count data
buildExonCountSet       Makes an ExonCountSet object from R objects.
constructModelFrame     Returns the model frame of an exonCountSet
                        object for the GLM fits.
countReadsForDEXSeq     Prepare annotation transcriptDb object for
                        DEXSeq.
countTableForGene       Count table for a given geneID.
counts                  Accessors for the 'counts' slot of a
                        ExonCountSet object.
design                  Accessor function for the design annotation
                        from a ExonCountSet object.
doCompleteDEUAnalysis   Perform complete differential exon usage
                        analysis
estimateDispersions     Estimate dispersions
estimateDispersions_BM
                        Estimate exon dispersions, using the deprecated
                        "big model" method
estimateExonDispersionsForModelFrame_BM
                        Estimates exon dispersions for the (deprecated)
                        "big model" method
estimateSizeFactors     Estimate the size factors for an ExonCountSet
estimatelog2FoldChanges
                        Fold changes (log2) from the fitted expression
                        values in the GLM.
exonIDs                 Accessor for the exonIDs in an ExonCountSet
                        object.
fitDispersionFunction   Fit the mean-variance function.
geneCountTable          Makes a count table for genes.
geneIDs                 Accessor for the geneIDs in an ExonCountSet
                        object.
makeCompleteDEUAnalysis_BM
                        Complete differential exon usage analysis
modelFrameForGene       Makes the model frame for a geneID.
newExonCountSet         Creates an ExonCountSet object
perGeneQValue           Summarize per-exon p-values into per-gene
                        q-values.
plotDEXSeq              Visualization of the fitted expression, fitted
                        splicing or the normalized counts.
plotDispEsts-methods    Diagnostic plot for dispersion estimates and
                        dispersion fit
plotMA-methods          Generate an MA plot
prepareAnnotationForDEXSeq-deprecated
                        Prepare annotation transcriptDb object for
                        DEXSeq.
read.HTSeqCounts        Read counts output from HTSeq script.
sizeFactors             Accessor functions for the sizeFactors
                        information in a ExonCountSet
subsetByGenes           Making an ExonCountSet object from another one
                        with a subset of its genes.
testForDEU              Test for Differential Exon Usage.
testForDEU_BM           Test for Differential Exon Usage (with the old,
                        deprecated "big model" approach.
testGeneForDEU_BM       Test a single gene for differential exon usage
                        using the old (and deprecated) "big model"
                        approach.
