This repository contain the pipeline, code for each analysis step, obtained results, and links to important resources required to develop the Bos taurus gene co-expression network to understand the pathogenesis of Rift Valley Fever
The topics covered include;
- 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/
- The original paper from which working data was obtained (Correlative Gene Expression to Protective Seroconversion in Rift Valley Fever Vaccinates)[https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147027]