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However, computational tools to detect differential chromatin contacts (DCCs) from scHi-C datasets in development and through disease pathogenesis are still lacking. Here, we present SnapHiC-D, a computational pipeline to identify DCCs between two scHi-C datasets. Compared to methods designed for bulk Hi-C data, SnapHiC-D detects DCCs with high sensitivity and accuracy. We used SnapHiC-D to identify cell-type-specific chromatin contacts at 10 Kb resolution in mouse hippocampal and human prefrontal cortical tissues, demonstrating that DCCs detected in the hippocampal and cortical cell types are generally associated with cell-type-specific gene expression patterns and epigenomic features. SnapHiC-D is freely available at https:\/\/github.com\/HuMingLab\/SnapHiC-D.<\/jats:p>","DOI":"10.1093\/bib\/bbad315","type":"journal-article","created":{"date-parts":[[2023,8,31]],"date-time":"2023-08-31T06:44:07Z","timestamp":1693464247000},"source":"Crossref","is-referenced-by-count":12,"title":["SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single-cell Hi-C data"],"prefix":"10.1093","volume":"24","author":[{"given":"Lindsay","family":"Lee","sequence":"first","affiliation":[{"name":"Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation , Cleveland, OH , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miao","family":"Yu","sequence":"additional","affiliation":[{"name":"Ludwig Institute for Cancer Research , La Jolla, CA , USA"},{"name":"State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University , Shanghai , 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China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongyu","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Wisconsin Madison , Madison, WI , USA"},{"name":"Department of Biochemistry, University of Wisconsin Madison , Madison, WI , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziyin","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University , Shanghai , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shreya","family":"Mishra","sequence":"additional","affiliation":[{"name":"Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation , Cleveland, OH , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bing","family":"Ren","sequence":"additional","affiliation":[{"name":"Ludwig Institute for Cancer Research , La Jolla, CA , USA"},{"name":"Center for Epigenomics & Department of Cellular and Molecular Medicine, University of California , San Diego, La Jolla, CA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of North Carolina , Chapel Hill, NC , USA"},{"name":"Department of Genetics, University of North Carolina , Chapel Hill, NC , USA"},{"name":"Department of Computer Science, University of North Carolina , Chapel Hill, NC , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0987-2916","authenticated-orcid":false,"given":"Ming","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation , Cleveland, OH , 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