/PyWGCNA

PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)

Primary LanguageJupyter NotebookMIT LicenseMIT

PyWGCNA

PyWGCNA is a Python library designed to do weighted correlation network analysis (WGCNA). It can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Users can also compare WGCNA networks from different datasets, or to external gene lists, to assess the conservation or functional enrichment of each module.

PyWGCNA overview

Documentation

PyWGCNA's full documentation can be found here

Installation

To install PyWGCNA, Python version 3.10 or greater is required.

Install from PyPi (recommended)

To install the most recent release, run

pip install PyWGCNA

Install with the most recent commits

pip install .

Tutorials

Suggested Reading

If you are unfamiliar with R refrence WGCNA, we suggest reading the original WGCNA publication:

Cite

PyWGCNA is now online in Bioinformatics. Please cite our paper when using PyWGCNA:

Narges Rezaie and others, PyWGCNA: A Python package for weighted gene co-expression network analysis, Bioinformatics, 2023; https://doi.org/10.1093/bioinformatics/btad415