Work

DiffHiChIP: Identifying differential chromatin contacts from HiChIP data

Year: 2025

Type: article

Abstract: This repository contains the source code and data related to the manuscript: Sourya Bhattacharyya, Daniela Salgado Figueroa et al., DiffHiChIP: Identifying differential chromatin contacts from HiChIP data AbstractChromatin conformation capture (3C) assays such as HiChIP are widely used to study interactions between cis-regulatory and structural elements. However, robust methods for detecting condition-specific loops remain limited. We introduce DiffHiChIP, the first comprehensive framework to call differential loops from HiChIP and similar 3C protocols. DiffHiChIP supports DESeq2 and edgeR using either complete contact map or a subset of contacts for background estimation, incorporates edgeR with generalized linear model (GLM) using either quasi-likelihood F-test or likelihood ratio test, and implements independent hypothesis weighting (IHW) as well as a distance stratification technique for modeling distance decay of contacts in estimating statistical significance. Our results on 5 datasets suggest that edgeR GLM-based models with IHW correction reliably capture differential interactions, including long-range, that are supported by published Hi-C data and reference studies. As HiChIP data become increasingly used for modeling chromatin regulation, DiffHiChIP promises to have a broad impact and utility.

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.17410329

Authors: Bhattacharyya, Sourya, Salgado Figueroa, Daniela, Georgopoulos, Katia, Ay, Ferhat

Institutions: La Jolla Institute for Immunology, University of California San Diego, Harvard University, Massachusetts General Hospital

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

OpenAlex ID: W7093351707

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