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netZooPy is a catalog of methods for the reconstruction and analysis of gene regulatory networks.

Available animals are: (gpu)PANDA, (gpu)LIONESS, (gpu)PUMA, SAMBAR, CONDOR, OTTER, and DRAGON.

netZooPy has merged of the following repositories and forks:

  • pypanda from David Van Ijzendorn,

  • Alessandro Marin’s pypanda and Marieke Kuijjer’s pypuma fork, and

  • Cho-Yi Chen’s fork.

  • Genis Calderer’s pysambar and pycondor

Getting started

Documentation

Netzoopy also has a command line interface that allows to run the animal methods from the command line, for example:

netzoopy panda --e expression.txt --m motif.txt --p ppi.txt --o output_panda.txt

Check the documentation below for a full list of options.

Indices and tables