The network zoo
netZoo{R,Py,M,C} is a menagerie of network biology methods. Implementation details and use cases in
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Ben Guebila et al, 2023. Genome Biology. doi:10.1186/s13059-023-02877-1
If you use netZoo, please cite us using the following format:
We used TIGER (Chen and Padi, 2024) as implemented in netZooR v 1.4 (Ben Guebila et al, 2023) and R v 4.2.
See the following citation example for reference.
A collection of tutorials is hosted on Netbooks, a cloud server that allows to run code without installing dependencies. It is possible to run these tutorials locally on a computer using R markdown, Jupyter notebooks, and LiveScript.
netZoo ecosystem
-
Methods are available as a web interface through netZooCloud beta! .
-
The software tools are developed in netZoo. Publication
-
Continuous integration is enabled through ZooKeeper (Travis-CI and GitHub actions).
-
A set of networks generated using netZoo methods 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) - coverage
C - build status (Ubuntu, Macos) - coverage
netZoo{R,Py,M,C} is a community maintained package licensed under GPL-3.0.
Labs
