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The network zoo

netZoo{R,Py,M,C} is a network biology package for the reconstruction and analysis of gene regulatory networks.

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

We used ALPACA (Padi and Quackenbush 2018) as implemented in netZooR (v 0.7.2; netzoo.github.io) using R (v 4.0.2).

See the following citation example for reference.

The package comes with a collection of tutorials in R markdown, Jupter notebooks, and LiveScript and many networks generated using the netZoo are available in GRAND database.

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 is enabled for netZoo using Travis and ZooKeeper.

R           - build status (Ubuntu) - 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