WGCNA and Module Preservation

This repository demonstrates a complete Weighted Gene-Co-expression Network Analysis (WGCNA) pipeline, including module preservation across datasets.

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1 Dataset

1. Download GeneExpression.zip.
2. Unzip it in the project root – you should end up with:

GeneExpression/
├── OSCC_TCGA_gene_expression_337.csv
├── OSCC_TCGA_gene_expression_32.csv

2 Code

wgcna.R

1. Pre-processes the expression matrix
2. Builds the WGCNA network
3. Calculates module eigengenes
4. Performs module-preservation analysis

3 How to run

1. Place wgcna.R in the same directory alongside the GeneExpression/ folder.
2. Open the script in RStudio to run the code

Citation

If you use this repository or the pipeline in your research, please cite:

Nguyen, P. and Zeng, E. (2025). A Protocol for Weighted Gene Co-expression Network Analysis With Module Preservation and Functional Enrichment Analysis for Tumor and Normal Transcriptomic Data. Bio-protocol, 15(18): e5447. https://doi.org/10.21769/BioProtoc.5447