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's full documentation can be found here
To install PyWGCNA, Python version 3.10 or greater is required.
To install the most recent release, run
pip install PyWGCNA
PyWGCNA
directory, and runpip install .
If you are unfamiliar with R refrence WGCNA, we suggest reading the original WGCNA publication:
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