Solas - Analysis of Alternative Splicing with short read data

*Solas home* | Installation | About RNA-Seq

Solas is a package for the statistical language R, devoted to the analysis of next generation short read data of transcripts, generally called RNA-Seq (see About RNA-Seq). Given gene annotation the major questions addressed by the package are:

prediction of alternative exons in a single condition / cell sample

prediction of differential alternative exons between two conditions / cell samples

quantification of alternative splice forms in a single condition / cell sample

Solas has been designed to analyze transcript data primarily derived from RNA-Seq experiments as it utilises count statistics, see the Installation page.

News

2010-10-12: Version 0.2.1 of Solas released. With a couple of changes:

- small bugs in the DASI-CASI estimation fixed
- more verbose output for errors
- if exact estimation is not feasible for DASI estimation, bootstrapping is used as an alternative to derive a p-value

2010-10-5: Solas will be extended to support splice junction and paired-end read connections in the near future.

2009-07-22: The bootstrap method for POEM is now explained in the tutorial.

2009-07-17: A tutorial for Solas has been introduced and can be found on the installation page.

2009-07-8: The Solas R-package is now online. See the Installation page for instruction to install the package on your local R version.

References

Solas was developed by Hugues Richard and Marcel Schulz at the Max Planck Institute for Molecular Genetics in Berlin, Germany.

Whenever you use Solas please cite:

Hugues Richard*, Marcel H. Schulz*, Marc Sultan*, Asja Nuernberger, Sabine Schrinner, Daniela Balzereit, Emilie Dagand, Axel Rasche, Hans Lehrach, Martin Vingron, Stefan A. Haas, and Marie-Laure Yaspo (2010)
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments
Nucleic Acids Research, 38 (10):e112 [full text]
*joint first authors