All our software is available through the lab bitbucket page: https://bitbucket.org/regulatorygenomicsupf/
Important: We are slowly migrating all our software to a new web page: https://github.com/comprna/
Software, databases and web services provided by the group:
- SUPPA: a tool for the fast calculation of alternative splicing patterns and differential splicing across at event and transcript level across multiple conditions from RNA-Seq data (source code) (Alamancos, Pagès et al. 2015) See new developments in this preprint.
- SPADA Notebook of Climente-Gonzalez et al. 2017. Software tools to describe transcript isoform switches per patient and calculating their functional impacts.
- MIRA (Mutation identification for RNA alterations). (soon available on biorxiv).
- MoSEA: Motif Scan and Enrichment Analysis tool (Used in Sebestyen et al. 2016, Trincado et al. 2017, Middleton et al. 2017) (source code).
- Junckey: Tool-set for the analysis of RNA-seq read junction clusters (source code).
- Iso-kTSP: a rank-based algorithm for the analysis of differential transcript usage between two conditions using many samples per condition (source code) (Sebestyén et al. 2015)
- Pyicos (PYICOTEO): a software tool for the analysis of ChIP-Seq and CLIP-Seq mapped reads (source code) (documentation) (google group) (Althammer, Gonzalez-Vallinas et al. 2011)
- SVM-BPfinder: a tool for mammalian U2 branch point prediction (source code) (web tool) (Corvelo et al. 2010). You can find a docker implementation here and the docker image here (thanks to Michael Lovci).
- ProfileSeq: a computational method for the quantitative assessment of biological profiles (source code)
- YISD: A database with information on RNA secondary structure of introns in S. cerevisiae and other Saccharomyces species (web) (Plass et al. 2012)
- BioMart server: A database of processed high-throughput epigenomics data used to study the relation between chromatin and splicing (Biomart server) (Allo, Agirre et al. 2014).