Code to generate the data and website for Rat TWAS Hub

Code for running large-scale multi-modal TWAS analyses in rat and producing static Markdown reports. This repository contains scripts that compute TWAS statistics for many traits, merge and annotate them, produce reports, and generate an interactive website. This code is adapted from the (human) TWAS HUB. It extends gene expression-based TWAS to multimodal RNA phenotypes (xTWAS) using Pantry to generate the transcriptome models.

The code uses the following parameter files:

• panels.par: Statistics on the transcriptome reference panels used. A MODALITY column has been added for xTWAS.
• all_models.par: Statistics on each of the predictive models. The Snakefile assembles this from the FUSION profiler script outputs.
• traits.par: Information on each of the traits/TWAS studies performed. Important, the OUTPUT column must to point to the merged results from all chromosomes for that trait.
• gene_names.tsv: Lookup table to convert the Ensembl IDs in the results to gene symbols for the site. The Snakefile assembles this from a gene annotation GTF file.

• Use Snakemake with the included Snakefile to run TWAS (FUSION) and post-processing.
• Run scripts/build_jekyll.sh to generate the Jekyll template.
• cd jekyll and then bundle exec jekyll build to generate the site.