Analysis code for the ENCODE distal regulation companion paper

This repository contains analysis code for analyses presented in the ENCODE distal regulation companion paper. Analyses can be found in following subdirectories:

crispr_analyses:

Snakemake workflow for CRISPR benchmarking and other related analyses results shown in Main Figures 1, 2, 4 and 5, Extended Data Figures 1, 2, 3, 7, Supplementary Figures S1.1, S1.2, S7, S8, S9, S10, as well as Supplementary Tables S2, S9, S10, S14, S15, S16.

process_dnase_metadata:

Code to process DNase-seq metadata from the ENCODE portal to select input files to generate ENCODE-rE2G predictions for 1,458 human DNase-seq experiments.