{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T18:22:36Z","timestamp":1771957356740,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T00:00:00Z","timestamp":1697500800000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute of Health","award":["R35GM133678"],"award-info":[{"award-number":["R35GM133678"]}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-1751317"],"award-info":[{"award-number":["DBI-1751317"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,10,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Here, we presented the scHiCDiff software tool that provides both nonparametric tests and parametirc models to detect differential chromatin interactions (DCIs) from single-cell Hi-C data. We thoroughly evaluated the scHiCDiff methods on both simulated and real data. Our results demonstrated that scHiCDiff, especially the zero-inflated negative binomial model option, can effectively detect reliable and consistent single-cell DCIs between two conditions, thereby facilitating the study of cell type-specific variations of chromatin structures at the single-cell level.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>scHiCDiff is implemented in R and freely available at GitHub (https:\/\/github.com\/wmalab\/scHiCDiff).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad625","type":"journal-article","created":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T19:46:27Z","timestamp":1697571987000},"source":"Crossref","is-referenced-by-count":8,"title":["scHiCDiff: detecting differential chromatin interactions in single-cell Hi-C data"],"prefix":"10.1093","volume":"39","author":[{"given":"Huiling","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Statistics, University of California Riverside , Riverside, CA 92521, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4097-1621","authenticated-orcid":false,"given":"Wenxiu","family":"Ma","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of California Riverside , Riverside, CA 92521, United States"}]}],"member":"286","published-online":{"date-parts":[[2023,10,17]]},"reference":[{"key":"2023102510225257700_btad625-B1","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1186\/s12859-016-0944-6","article-title":"Discrete distributional differential expression (D3E)-a tool for gene expression analysis of single-cell RNA-seq data","volume":"17","author":"Delmans","year":"2016","journal-title":"BMC 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computational pipeline to identify chromatin loops from single-cell HI-C data","volume":"18","author":"Yu","year":"2021","journal-title":"Nat Methods"},{"key":"2023102510225257700_btad625-B12","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1186\/s13059-022-02774-z","article-title":"Normalization and de-noising of single-cell HI-C data with bandnorm and SCVI-3D","volume":"23","author":"Zheng","year":"2022","journal-title":"Genome 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