counts | Accessors for the 'counts' slot of a ExonCountSet object. |
counts-method | Accessors for the 'counts' slot of a ExonCountSet object. |
counts<--method | Accessors for the 'counts' slot of a ExonCountSet object. |
countTableForGene | Count table for a given geneID. |
design | Accessor function for the design annotation from a ExonCountSet object. |
design-method | Accessor function for the design annotation from a ExonCountSet object. |
design<--method | Accessor function for the design annotation from a ExonCountSet object. |
DEUresultTable | Get a result table from the analysis workflow. |
DEXSeqHTML | HTML report writer |
estimateDispersions | Estimate exon dispersions |
estimateDispersions-method | Estimate exon dispersions |
estimateExonDispersionsForModelFrame | Estimates exon dispersions |
estimatelog2FoldChanges | Fold changes (log2) from the fitted expression values in the GLM. |
estimateSizeFactors | Estimate the size factors for an ExonCountSet |
estimateSizeFactors-method | Estimate the size factors for an ExonCountSet |
ExonCountSet-class | "ExonCountSet", a container for exon count data |
exonIDs | Accessor for the exonIDs in an ExonCountSet object. |
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. |
geneIDs<- | Accessor for the geneIDs in an ExonCountSet object. |
makeCompleteDEUAnalysis | Complete differential exon usage analysis |
modelFrameForGene | Makes the model frame for a geneID. |
newExonCountSet | Creates an ExonCountSet object |
plotDEXSeq | Visualization of the fitted expression, fitted splicing or the normalized counts. |
read.HTSeqCounts | Read counts output from HTSeq script. |
sizeFactors | Accessor functions for the sizeFactors information in a ExonCountSet |
sizeFactors-method | Accessor functions for the sizeFactors information in a ExonCountSet |
sizeFactors<--method | 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. |
testGeneForDEU | Test a single gene for differential exon usage. |