SwitchSeq

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A tool to identify, annotate and visualise splicing switch events from RNA-seq data

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## SwitchSeq
When working with RNA-seq data, several tools exist to quantify differences in splicing across conditions and to address the significance of those changes (e.g. [DEXSeq](http://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html), [MMDIFF](http://www.ncbi.nlm.nih.gov/pubmed/24281695)). Quiet often though, these tools result in a long list of genes that is difficult to interpret. By relying on transcript level quantifications, SwitchSeq provides a simple (yet powerful) approach to identify, annotate and visualise the most extreme changes in splicing across two different conditions, namely **switch events**. In brief, switch events are defined as those cases where, for a given gene, the identity of the most abundant transcript changes across conditions:

![SwitchSeq overview](https://raw.githubusercontent.com/mgonzalezporta/SwitchSeq/master/doc/fig1.png)

*Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq.*
Mar Gonzàlez-Porta, Alvis Brazma.
[Available in bioRxiv](http://dx.doi.org/10.1101/005967).

[Related slides available in Slideshare](http://www.slideshare.net/MarGonzlezPorta/identification-annotation-and-visualisation-of-extreme-changes-in-splicing-with-switchseq)

## Quick navigation
* [Setup guide](https://github.com/mgonzalezporta/switchseq/wiki/Setup-guide)
* [Tutorial](https://github.com/mgonzalezporta/switchseq/wiki/Tutorial)
* [Software usage](https://github.com/mgonzalezporta/switchseq/wiki/Software-usage)

## License
SwitchSeq is licensed under GPLv2.

## Contact
Mar Gonzàlez-Porta:
<mar@ebi.ac.uk>

SwitchSeq

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