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Find splicing-led, functional changes of the proteome.

Project description

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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.

Project details


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Filename, size & hash SHA256 hash help File type Python version Upload date
spada-1.23.7-py3-none-any.whl (67.6 kB) Copy SHA256 hash SHA256 Wheel py3 Jul 23, 2018

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