Github repo for Anderson et al. 2022 (DOI: https://doi.org/10.1098/rstb.2020.0441)

Github repository for results and figures from Anderson et al. "Distinct gene regulatory signatures of dominance rank and social bond strength in wild baboons".

This github repo contains 4 major chunks:

1. preprocessing.R -- This script contains pre-processing of raw counts. This code can be skipped, as residual gene expression is also provided within this repo.

2. linear_models.R -- This script contains the linear mixed models run to obtain gene-by-gene estimates of rank and social bond strength effects on gene expression and gene expression responses.

3. predictions.R -- This script contains elastic net regularization code for predicting dominance rank from gene expression values.

4. gene_set_enrichment_analyses.R -- This script contains code for Gene Set Enrichment Analyses. The original GSEA scripts which I wrote a wrapper on top of are available at https://github.com/GSEA-MSigDB/GSEA_R.