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Pypath

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Offers advanced possibilities for pathway analysis. Pypath builds up networks from multiple sources on one igraph object, handles ambiguous ID conversion, reads custom edge and node attributes from text files and MySQL. Pypath automatically updates its content, which is dynamically gathered from resources. It is also capable of compiling networks from custom sets of interaction resources and can integrate additional annotations.

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Pypath classification

Pypath specifications

Software type:
Application/Script
Restrictions to use:
None
Programming languages:
Python
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 3.0
Version:
0.5.0
Requirements:
cairo, py(2)cairo, igraph, python(2)-igraph, graphviz, pygraphviz

Pypath distribution

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Pypath support

Maintainers

  • denes <>
  • Julio Saez-Rodriguez <>

Additional information

http://pypath.omnipathdb.org/

Credits

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Publications

Institution(s)

European Molecular Biology Laboratory–European Bioinformatics Institute, Hinxton, UK; Earlham Institute, Norwich, UK; Institute of Food Research, Norwich, UK; RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine, Aachen, Germany

Funding source(s)

This work was supported by the EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Skłodowska-Curie COFUND Actions (grant number 291772), a fellowship in computational biology at the Earlham Institute (Norwich, UK) in partnership with the Institute of Food Research (Norwich, UK), and strategically supported by Biotechnological and Biosciences Research Council, UK (BB/J004529/1).

Link to literature

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