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Description

netZooR is an R package to construct, analyse and plot gene regulatory networks.

Features

netZooR currently integrates with:

• PANDA(Passing Attributes between Networks for Data Assimilation)[Glass et al. 2013]: construct gene regulatory network from gene expression data, protein-protein interaction data, and transcription factor binding motifs (TFBMs) data.

• CONDOR(COmplex Network Description Of Regulators)[Platig et al. 2016]: analyse bipartite community structure analysis of biological networks.

• LIONESS(Linear Interpolation to Obtain Network Estimates for Single Samples)[Kuijjer et al. 2019]: reconstruct single-sample gene regulatory networks.

• ALPACA(ALtered Partitions Across Community Architectures)[Padi and Quackenbush 2018]: compare two networks and identify changes in modular structure.

• SAMBAR(Subtyping Agglomerated Mutations By Annotation Relations)[Kuijjer et al.]: identify subtypes based on somatic mutation data.

• Source protein-protein interaction network from STRINGdb based on a list of protein of interest.

• Plot one PANDA network in Cytoscape.

• Plot two differential PANDA networks in Cytoscape.

Installation

# install.packages("devtools") 
library(devtools)
# install netZooR pkg with vignettes, otherwise remove the "build_vignettes = TRUE" argument.
devtools::install_github("netZoo/netZooR", build_vignettes = TRUE)

Quick Starts & tutorials

Please refer to the top navigation bar Articles/Quick-Starts for basic usage and application cases. Or use browseVignettes("netZooR") after installing package.

Development

Contributions are welcome! Instruction of how to contribute netZooR repository can be found here. The master branch on github should always be in good shape, so please to pull request to the devel branch.

Issues

For data.table installation issue please refer to issue #40.

Please report any further issue to the issues page.

License

The software is free and is licensed under the GNU General License v3.0, see the file LICENSE for details.

Code of conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.