spada

spada (Splicing-led Protein Alterations Discovered Agilely) is a tool to study the functional impact of alternative splicing changes in case-control studies. The alterations are represented as isoform switches i.e. the situation when cases are best represented by one isoform, while controls are best represented by a different one. Then, spada is able to predict which protein features are changing between both isoforms, and their impact on the protein-protein interaction network.

To start using spada, simply install it with

pip install spada

This package has two main functionalities:

• Calculating isoform switches from case-control transcript expression data:

  spada switches --expression-control expression_ctrl.tsv \
    --expression-case expression_case.tsv --minimum-expression 0.1
  

• Predicting the effects of splicing on the protein structure and the interactome of a set of switches:

  spada function --switches switches.tsv
  

For detailed information on how to use spada, please visit the wiki.

Documentation

Citation

If you use spada in a scientific publication, we would appreciate citations:

Climente-González, H., Porta-Pardo, E., Godzik, A., and Eyras, E. (2017). The Functional Impact of Alternative Splicing in Cancer. Cell Reports 20, 2215–2226.

Related projects

• smartas: we applied spada to transcriptomics data from the TCGA. This repository contains the code for the analyses and the main conclusions.