This repository contains all scripts for anlaysis + tissue-type specific source data for DHS footprinting data.
Lung DHS data can be found in lung_footprint_data/lung_union_data.
Lymphocyte DHS data can be found in lymphocyte_data.
Consensus DHS data is available in the dhs.rdata file. \
Consensus DHS footprints are available for download here (https://www.vierstra.org/resources/dgf#downloads).
GTEx v8 eQTL and sQTL eGenes and sGenes are available for download here (https://www.gtexportal.org/home/downloads/adult-gtex/qtl).
NHGRI GWAS catalog is available for download here (https://www.ebi.ac.uk/gwas/).
gtex_blood_enrichment.R and gtex_lung_enrichment.R corresponds to analysis scripts for Figure 6a and 6b respectively.
consensus_gwas_enrichment.Rcorresponds to analysis scripts for Figure 6c.
all_eQTL_sQTL.Rcorresponds to analysis scripts for Figure 6d-6e.
The 1000G Phase 3 EUR panel is split by chromosome in the thousand_genome_panel_hg38_by_chr folder. These files can be concatenated to create a comprehensive panel.
All bootstrap test results are available in the enrichment_results folder. The create_boxplot.R provides the code for creating the figures. The produced figures are all available in enrichment_figures.