OAK_scripts contains the scripts used to do positive selection computation on Sherlock, Stanford's computer cluster. This includes computing confidence intervals for a variety of sets of genes of interest etc. You can use create_run_scripts.py to create scripts to run everything.

GenomeWide_JASPAR_TFBS_SNPs contains its own README and was used to call TFBS in humans and various NHPs

Computing_PhyloP contains the code used to compute PhyloP scores and has its own README

Figures_Analysis contains the code used to do analysis after running things on the computer cluster and make figures and has its own README

Human_Substitution_Processing contains the code used to process the human polymorphic/fixed substitution data and has its own README

Postprocessing_DL_Predictions contains code to compute cell type-specificity scores from ChromBPNet output

Processing_ATAC_Data contains the code used to process the ATAC data for input to ChromBPNet

Pteropus_alecto contains the code used to analyze black flying fox data

Simulations contains the code used to do the simulations in slim