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| buildExonCountSet | This functions are deprecated and will become defunct. |
| buildExonCountSet-deprecated | This functions are deprecated and will become defunct. |
| constructModelFrame | This functions are deprecated and will become defunct. |
| constructModelFrame-deprecated | This functions are deprecated and will become defunct. |
| countReadsForDEXSeq | This functions are defunct and will be deleted |
| countReadsForDEXSeq-defunct | This functions are defunct and will be deleted |
| counts | Accessors for the 'counts' slot of a DEXSeqResults object. |
| counts,ExonCountSet-method,deprecated | Accessors for the 'counts' slot of a DEXSeqResults object. |
| counts-method | Accessors for the 'counts' slot of a DEXSeqResults object. |
| countTableForGene | This functions are deprecated and will become defunct. |
| countTableForGene-deprecated | This functions are deprecated and will become defunct. |
| design,ExonCountSet | This functions are deprecated and will become defunct. |
| design,ExonCountSet-deprecated | This functions are deprecated and will become defunct. |
| DEUresultTable | This functions are deprecated and will become defunct. |
| DEUresultTable-deprecated | This functions are deprecated and will become defunct. |
| DEXSeq | Performs the differential exon usage test in a single command |
| DEXSeq-defunct | This functions are defunct and will be deleted |
| DEXSeq-deprecated | 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 |
| doCompleteDEUAnalysis | This functions are deprecated and will become defunct. |
| doCompleteDEUAnalysis-deprecated | This functions are deprecated and will become defunct. |
| estimateDispersions | Estimate the dispersions for a DEXSeqDataSet |
| estimateDispersions,ExonCountSet-method-deprecated | Estimate the dispersions for a DEXSeqDataSet |
| estimateDispersions-method | Estimate the dispersions for a DEXSeqDataSet |
| estimateDispersions_BM | This functions are deprecated and will become defunct. |
| estimateDispersions_BM-deprecated | This functions are deprecated and will become defunct. |
| estimateExonDispersion | This functions are deprecated and will become defunct. |
| estimateExonDispersion-deprecated | This functions are deprecated and will become defunct. |
| estimateExonDispersionsForModelFrame_BM | This functions are deprecated and will become defunct. |
| estimateExonDispersionsForModelFrame_BM-deprecated | This functions are deprecated and will become defunct. |
| estimateExonFoldChanges | Estimates exon usage coefficients from the fitted terms of the GLM. |
| estimatelog2FoldChanges | This functions are deprecated and will become defunct. |
| estimatelog2FoldChanges-deprecated | This functions are deprecated and will become defunct. |
| estimateSizeFactors | Estimate the size factors for a DEXSeqDataSet |
| estimateSizeFactors,ExonCountSet-method,deprecated | Estimate the size factors for a DEXSeqDataSet |
| estimateSizeFactors-method | Estimate the size factors for a DEXSeqDataSet |
| ExonCountSet | This class has been deprecated and will become defunct. |
| ExonCountSet-class | This class has been deprecated and will become defunct. |
| 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 |
| fitDispersionFunction | This functions are deprecated and will become defunct. |
| fitDispersionFunction-deprecated | This functions are deprecated and will become defunct. |
| geneCountTable | This functions are deprecated and will become defunct. |
| geneCountTable-deprecated | This functions are deprecated and will become defunct. |
| geneIDs | Accessor functions for DEXSeqDataSet details |
| geneIDs<- | Accessor functions for DEXSeqDataSet details |
| getCountVector | This functions are deprecated and will become defunct. |
| getCountVector-deprecated | This functions are deprecated and will become defunct. |
| groupIDs | Accessor functions for DEXSeqDataSet details |
| groupIDs<- | Accessor functions for DEXSeqDataSet details |
| makeCompleteDEUAnalysis_BM | This functions are deprecated and will become defunct. |
| makeCompleteDEUAnalysis_BM-deprecated | This functions are deprecated and will become defunct. |
| modelFrameForGene | This functions are deprecated and will become defunct. |
| modelFrameForGene-deprecated | This functions are deprecated and will become defunct. |
| newExonCountSet | This functions are deprecated and will become defunct. |
| newExonCountSet-deprecated | This functions are deprecated and will become defunct. |
| perGeneQValue | Summarize per-exon p-values into per-gene q-values. |
| plotDEXSeq | Visualization of the per gene DEXSeq results. |
| plotDispEsts | Plot dispersion estimates |
| plotDispEsts,ExonCountSet-method,deprecated | Deprecated methods for ExonCountSet object |
| plotDispEsts-method | Deprecated methods for ExonCountSet object |
| plotDispEsts-method | Plot dispersion estimates |
| plotMA | Generate an MA plot |
| plotMA,ExonCountSet | Deprecated methods for ExonCountSet object |
| plotMA,ExonCountSet-deprecated | Deprecated methods for ExonCountSet object |
| plotMA,ExonCountSet-method,deprecated | Generate an MA plot |
| plotMA-method | Generate an MA plot |
| plotMA-methods | Generate an MA plot |
| prepareAnnotationForDEXSeq | This functions are defunct and will be deleted |
| prepareAnnotationForDEXSeq-defunct | This functions are defunct and will be deleted |
| read.HTSeqCounts | This functions are deprecated and will become defunct. |
| read.HTSeqCounts-deprecated | This functions are deprecated and will become defunct. |
| sampleAnnotation | Accessor functions for DEXSeqDataSet details |
| sizeFactors,ExonCountSet-method,deprecated | Deprecated methods for ExonCountSet object |
| sizeFactors-method | Deprecated methods for ExonCountSet object |
| subsetByGenes | This functions are deprecated and will become defunct. |
| subsetByGenes-deprecated | This functions are deprecated and will become defunct. |
| 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 |
| testExonForDEU | This functions are deprecated and will become defunct. |
| testExonForDEU-deprecated | This functions are deprecated and will become defunct. |
| testForDEU | Test for Differential Exon Usage. |
| testForDEU_BM | This functions are deprecated and will become defunct. |
| testForDEU_BM-deprecated | This functions are deprecated and will become defunct. |
| testGeneForDEU_BM | This functions are deprecated and will become defunct. |
| testGeneForDEU_BM-deprecated | This functions are deprecated and will become defunct. |