The repository contains code related to the methods from the article "Long-range regulatory effects of Neandertal DNA in modern humans"
a) haplotype_inferring folder includes an algorithm for the annotation of archaic haplotypes in cohorts used in this study
b) collapsing_SNPs_R2 includes an algorithm for generating a dataset of sets of LD-collapsed variants
c) TF_prediction_DBs describes the generation of a concordant TFs database from Human_TFTG and Harmonizome TF target databases
d) TF_target_enrichment folder describes a test for the analyses of TF target genes enrichment in Neandertal deserts and random genomic regions
e) aSNPs_proportion_enrichment performs enrichment analysis of the relative number of significant trans-eQTL associations for Neandertal variants compared to frequency-matched non-archaic variants
f) effect_sizes-cTFs_GTEx_eQTLGen performs correlation analysis of effect sizes between eQTLGen and GTEx cis-eQTLs for shared cTFs