Input files for this analysis can be obtained from zenodo.
TFBS enrichment via Snakemake, see Snakefile.
Cis-regulatory element enrichment uses these scripts:
- Overlap in EPIC pairs:
R/cre_enrichment/annotation_overlap_EPIC.R - Overap for background pairs:
R/cre_enrichment/annotation_overlap_EPIC_background.R - Helper methods for enrichment:
R/cre_enrichment/annotation_overlap_methods.R