Package index
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DEXSeq-defunct - This functions are deprecated and will become defunct.
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DEXSeq() - Performs the differential exon usage test in a single command
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DEXSeqDataSet()DEXSeqDataSetFromHTSeq()DEXSeqDataSetFromSE() - DEXSeqDataSet object and constructors
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DEXSeqHTML() - DEXSeq HTML report writer
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DEXSeqResults() - DEXSeqResults object
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featureCounts()featureIDs()`featureIDs<-`()exonIDs()`exonIDs<-`()groupIDs()`groupIDs<-`()geneIDs()`geneIDs<-`()sampleAnnotation() - Accessor functions for DEXSeqDataSet details
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counts(<DEXSeqResults>) - Accessors for the 'counts' slot of a DEXSeqResults object.
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estimateDispersions(<DEXSeqDataSet>) - Estimate the dispersions for a DEXSeqDataSet
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estimateExonFoldChanges() - Estimates exon usage coefficients from the fitted terms of the GLM.
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estimateSizeFactors(<DEXSeqDataSet>) - Estimate the size factors for a DEXSeqDataSet
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subsetByOverlaps(<DEXSeqResults>,<GenomicRanges>)findOverlaps(<DEXSeqResults>,<GenomicRanges>) - Methods from GRanges overlaps for the DEXSeq object
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`[`(<DEXSeqDataSet>)`$<-`(<DEXSeqDataSet>) - Subset and replacements of DEXSeqDataSet slots
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perGeneQValue() - Summarize per-exon p-values into per-gene q-values.
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plotDEXSeq() - Visualization of the per gene DEXSeq results.
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plotDispEsts(<DEXSeqDataSet>) - Plot dispersion estimates
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plotMA(<DEXSeqDataSet>)plotMA(<DEXSeqResults>) - Generate an MA plot
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testForDEU() - Test for Differential Exon Usage