Metadata-Version: 2.1
Name: spada
Version: 1.21.18
Summary: Find splicing-led, functional changes of the proteome.
Home-page: https://github.com/hclimente/spada
Author: Héctor Climente-González
Author-email: hector.climente@curie.fr
License: MIT
Download-URL: https://github.com/hclimente/spada/archive/v1.9.1.tar.gz
Keywords: alternative,splicing,analysis,transcriptomics,networks
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3 :: Only
Description-Content-Type: text/markdown
Requires-Dist: networkx (>=1.11)
Requires-Dist: numpy (>=1.13.1)

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## spada

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.

To start using spada, simply install it with

``` bash
pip install spada
```

spada has three main functions:

``` bash
# import data into spada's data-structures
spada init --help

# calculate isoform switches from case-control transcriptomics data
spada switches --help

# predict effects of splicing on the protein structure and the interactome
spada function --help
```

For detailed information on how to use spada, please visit the [wiki](https://github.com/hclimente/spada/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.]((http://www.cell.com/cell-reports/abstract/S2211-1247(17)31104-X)) Cell Rep. 20, 2215–2226.

#### Related projects

* [smartas](https://github.com/hclimente/smartas): we applied spada to transcriptomics data from the TCGA. This repository contains the code for the analyses and the main conclusions.


