This R script is to demonstrate Weighted Correlation Network Analysis (WGCNA) using R.
This is the repository of the files and R script needed for the tutorial in the Youtube Channel (Liquid Brain, https://www.youtube.com/c/LiquidBrain), the topics it covers are including:
- What data you need for WGCNA
- How to perform network construction and module detection
- How to export the network files for visualization in Cytoscape
- Correlate the modules with external trait (discrete type)
- Correlate the modules with external trait (continuous type)
- Further investigation on particular module-trait relationship
- Visualization (e.g. scatterplot, bubble plot)
- Summary of the whole WGCNA analysis
References:
- The original tutorial provided by the creators (Peter Langfelder and Steve Horvath) https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/
- A nice Nature Plants paper by Yu et al. https://www.nature.com/articles/s41477-021-00897-y (Check their "data availability" section for the link to the github R script)