Find splicing-led, functional changes of the proteome.
Project description
SPADA
WARNING: SPADA is still a work-in-progress. Take this README as a statement of intent.
SPADA (Splicing-led Protein Alterations Discovered Agilely) is a tool to study the functional impact of alternative splicing changes between two conditions. The alterations have to be represented as isoform switches i.e. when one condition is best represented by one isoform, and the second condition by another one. Then, SPADA is able to predict which protein features are changing between both isoforms, and their impact on the protein-protein interaction network. A SPADA-based analysis of isoform switches found in the TCGA dataset was published in Climente-González et al. (2017).
To start using SPADA, simply install it with
pip install spada
and run it in a toy dataset with
spada.py function --annotation gencode --switches spada.example
For information about how to run SPADA on your dataset, please read the documentation.
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