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| $<--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 |