DEXSeq

Detecting differential usage of exons from RNA-seq data

RNA-Seq is a powerful tool for the study of alternative splicing and other
forms of alternative isoform expression. Understanding the regulation of
these processes requires sensitive and specific detection of differential iso-
form abundance in comparisons between conditions, cell types or tissues.
We present DEXSeq, a statistical method to test for differential exon usage
in RNA-Seq data. DEXSeq employs generalized linear models and offers re-
liable control of false discoveries by taking biological variation into account.
DEXSeq detects genes, and in many cases specific exons, that are subject to
differential exon usage with high sensitivity. We demonstrate the versatility
of DEXSeq by applying it to several data sets. The method facilitates the
study of regulation and function of alternative exon usage on a genome-wide
scale. An implementation of DEXSeq is available as an R/Bioconductor
package.

http://genome.cshlp.org/content/early/2012/06/21/gr.133744.111.full.pdf+html

http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.html

HTSeq: Analysing high-throughput sequencing data with Python
http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html