DEXSeq is a statistical method to test for differential exon usage in RNA-seq data. DEXSeq uses generalized linear models and offers reliable control of false discoveries by taking biological variation into account.
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Genome Res. 2012 Oct;22(10):2008-17. doi: 10.1101/gr.133744.111. Epub 2012 Jun 21.
Detecting differential usage of exons from RNA-seq data.
Anders S, Reyes A, Huber W.