DEXSeq v1.18.4

by Alejandro Reyes

Inference of differential exon usage in RNA-Seq

The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

Functions in DEXSeq

Name Description
DEXSeq Performs the differential exon usage test in a single command
DEXSeqHTML DEXSeq HTML report writer
DEXSeq-defunct This functions are deprecated and will become defunct.
counts Accessors for the 'counts' slot of a DEXSeqResults object.
estimateExonFoldChanges Estimates exon usage coefficients from the fitted terms of the GLM.
plotDEXSeq Visualization of the per gene DEXSeq results.
DEXSeqResults-class DEXSeqResults object
findOverlaps Methods from GRanges overlaps for the DEXSeq object
DEXSeqDataSet-methods Subset and replacements of DEXSeqDataSet slots
estimateSizeFactors Estimate the size factors for a DEXSeqDataSet
DEXSeqDataSet-class DEXSeqDataSet object and constructors
perGeneQValue Summarize per-exon p-values into per-gene q-values.
featureCounts Accessor functions for DEXSeqDataSet details
plotDispEsts Plot dispersion estimates
testForDEU Test for Differential Exon Usage.
plotMA-methods Generate an MA plot
estimateDispersions Estimate the dispersions for a DEXSeqDataSet
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