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bioRxiv · 10.64898/2026.02.01.703086

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

Kim, S. S.·Jackson, J. T.·Zhang, H. B.·Kim, M.
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Abstract

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.

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Kim, S. S., Jackson, J. T., Zhang, H. B., Kim, M.. 2026-02-03. HiChIA-Rep quantifies the similarity between enrichment-based chromatin interactions datasets. https://doi.org/10.64898/2026.02.01.703086

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