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The network zoo

netZooR netZooPy netZooM netZooC Netbooks

netZoo{R,Py,M,C} is a network biology package for the inference and analysis of gene regulatory networks. Implementation details and use cases in

The Network Zoo: a multilingual package for the inference and analysis of biological networks. Ben Guebila et al, 2022. bioRxiv. doi:10.1101/2022.05.30.494077v1

If you use netZoo, please cite us using the following format:

We employed ALPACA (Padi and Quackenbush, 2018) as implemented in netZooR v 1.0 (Ben Guebila et al, 2022) using R v 4.0.2.

See the following citation example for reference.

A collection of tutorials hosted on the cloud allows you to get up and running without hardware requirement and without installing any depedency. netZoo R and Python tutorials are available on Netbooks. Otherwise, you can run the tutorials on your computer using R markdown, Jupyter notebooks, and LiveScript.

netZoo ecosystem

  • The software tools are developed in netZoo.

  • Continuous integration is enabled through ZooKeeper (Travis-CI, GitHub actions, and Jenkins).

  • A set of networks generated using netZoo tools are hosted in GRAND database. Publication.

  • netZoo tutorials are distributed through bundled hardware and software environments using Netbooks. Publication.

  • To ask questions or to provide feedback or ideas, please use our community channel for discussions.

Packages

R:             netZooR

Python:     netZooPy

MATLAB:   netZooM

C:             netZooC

Following the update of python-igraph package from 0.7.1.post6 to newer versions, the assignemnt of communities in condor as implemented in netZooPy has changed. netZooPy >= 0.7.2 imports newer versions of python-igraph > 0.7.1.post6, therefore the results of condor in netZooPy < 0.7.2 and netZooPy >= 0.7.2 could be different.

Starting from netZooM 0.4.1, netZooPy 0.5.1, and netZooR 0.6.1 (which includes pandaR 1.19.4), the default data processing step in PANDA has changed. Data processing was modified in all platforms to give the same output as PANDA in netZooC, which adds rows of zeros if a gene/TF is missing in at least one prior (expression, motif, ppi). The previous behavior can be accessed through the ‘legacy’ option in the variable mode. The option ‘intersection’ of the variable mode removes missing TFs/genes if they are absent from at least one prior.

Live status

Continuous integration (ZooKeeper) is enabled for netZoo using Travis for netZooC and netZooM, and GitHub actions for netZooR and netZooPy.

R           - build status (Ubuntu, Macos) - coverage

Python   - build status (Ubuntu, Macos) - coverage

MATLAB - build status (Ubuntu, Macos) - coverage

C           - build status (Ubuntu, Macos) - coverage

netZoo{R,Py,M,C} is a community maintained package licensed under GPL-3.0.

Labs

labs