A tutorial & literate programming guide to using WGCNA with expression data and annotations from EnTAP.
Large parts of this tutorial are adapted directly from Steve Horvath's WGCNA tutorial. The primary aim of this repository and tutorial is to aid those with de novo transcriptomes who have annotated those transcriptomes using EnTAP. The secondary aim of this repository is to serve as supplemental information for a forthcoming publication.
- Part 1: Load expression data and trait data
- Part 2: Pick soft-thresholding power and detect modules
- Part 3: Examine module/trait correlation
- Part 4: Incorporate annotations
- Part 5: Create visualization of TOM (optional)
I have added five R scripts -- WGCNA Modules 1-5 -- as demos of the WGCNA procedures outlined above. Full markdown of the scripts are forthcoming.