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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

• Installation guide
  • PIP installation
    • Requirements
    • Install
    • Troubleshooting
  • Conda installation

• Tutorials

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.

• Command Line Interface
  • Commands
    • netzoopy
      • panda
      • lioness
      • condor
  • Run functions (legacy)
    • Panda
    • Lioness

• The Animals (API)
  • Panda
  • Condor
    • Other function
  • Lioness
  • Puma
  • Sambar
    • Extra sambar functions

• Changelog
  • 0.9.6 (2022-06-10)
  • 0.9.5 (2022-05-24)
  • 0.9.4 (2022-05-20)
  • 0.9.2 (2022-03-04)
  • 0.9.0 (2022-02-11)
  • 0.8.0 (2021-06-08)
  • 0.7.2 (2020-07-18)
  • 0.7.1 (2020-06-27)
  • 0.7.0 (2020-01-18)
  • 0.6.2 (Stockholm) (2020-05-15)
  • 0.6.1 (2020-01-18)
  • 0.5.0 (2019-11-22)
  • 0.4.0 (2019-11-18)
  • 0.3.0 (2019-11-14)
  • 0.2.0 (2019-11-13)
  • 0.1.1 (2019-9-3)
  • 0.1.0 (2019-7-26)

Indices and tables

• Index

• Module Index

• Search Page