Software

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.
  • 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)
  • 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 from the ENCODE project for the development of predictive models of gene regulation. (Biomart server) (Althammer et al. 2012)