Inference of differential exon usage in RNA-Seq


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Documentation for package ‘DEXSeq’ version 1.12.2

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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.