This repository contains the relevant code for the major analyses in our manuscript:
Rare codon patches coordinate an RNA regulatory network and are impacted by repeat expansions linked to brain disorders
Fine et al. (2025)
We perform a systematic search and characterization of rare codon patches in human protein-coding genes, integrating data from ribosome profiling, RNA-protein mapping projects, human population genetics, and repeat expansions.
sequence_retrieval - processes genome annotation files to obtain coding sequences
sequence_processing - generates rare codon patches and matched controls
riboseq_analysis - analysis of ribosome occupancy
rbp_analysis - analysis of RNA-binding proteins (RBPs)
repeat_analysis - analysis of repeat expansions
population_genetics- analysis of human population genetics
For inquiries about this repository, feel free to reach out to [email protected]