{"doi":"10.1016/j.crmeth.2025.101214","title":"DiffHiChIP: Identifying differential chromatin contacts from HiChIP data","abstract":"Chromosome 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 a 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 five datasets suggest that edgeR GLM-based models with IHW correction reliably capture differential interactions, including long-range interactions, 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.","journal":"Cell Reports Methods","year":2025,"id":580067,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9471,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":908991,"name":"Daniela Salgado Figueroa","orcid":"0000-0001-6476-7612","position":1,"is_corresponding":false},{"id":492590,"name":"Katia Georgopoulos","orcid":"0000-0002-8963-4258","position":2,"is_corresponding":false},{"id":45041,"name":"Ferhat Ay","orcid":"0000-0002-0708-6914","position":3,"is_corresponding":false},{"id":266582,"name":"Sourya Bhattacharyya","orcid":"0000-0002-5767-8168","position":0,"is_corresponding":true}],"reference_count":51,"raw_metadata":null,"created_at":"2026-07-19T02:58:38.868285Z","pmid":"41187750","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}