HiChIA-Rep quantifies the similarity between enrichment-based chromatin interactions datasets

3D genome mapping technologies ChIA-PET, HiChIP, PLAC-seq, HiCAR, and ChIATAC yield pairwise contacts and a one-dimensional signal indicating protein binding or chromatin accessibility. However, a lack of computational tools to quantify the reproducibility of these enrichment-based 3C data prevents rigorous data quality assessment and interpretation. We developed HiChIA-Rep, an algorithm incorporating both 1D and 2D signals to measure similarity via graph signal processing methods. HiChIA-Rep can distinguish biological replicates from non-replicates, cell lines, and protein factors, outperforming tools designed for Hi-C data. With a large amount of multi-ome datasets being generated, HiChIA-Rep will likely be a fundamental tool for the 3D genomics community.