{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T18:56:02Z","timestamp":1773341762337,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,31]],"date-time":"2020-01-31T00:00:00Z","timestamp":1580428800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Institutes of Health Common Fund 4D Nucleome Project","award":["U01CA200059"],"award-info":[{"award-number":["U01CA200059"]}]},{"name":"Harvard College Research Program"},{"name":"Pechet Family Research Fund"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Single-cell Hi-C (scHi-C) allows the study of cell-to-cell variability in chromatin structure and dynamics. However, the high level of noise inherent in current scHi-C protocols necessitates careful assessment of data quality before biological conclusions can be drawn. Here, we present GiniQC, which quantifies unevenness in the distribution of inter-chromosomal reads in the scHi-C contact matrix to measure the level of noise. Our examples show the utility of GiniQC in assessing the quality of scHi-C data as a complement to existing quality control measures. We also demonstrate how GiniQC can help inform the impact of various data processing steps on data quality.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code and documentation are freely available at https:\/\/github.com\/4dn-dcic\/GiniQC.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa048","type":"journal-article","created":{"date-parts":[[2020,1,24]],"date-time":"2020-01-24T20:11:36Z","timestamp":1579896696000},"page":"2902-2904","source":"Crossref","is-referenced-by-count":10,"title":["GiniQC: a measure for quantifying noise in single-cell Hi-C data"],"prefix":"10.1093","volume":"36","author":[{"given":"Connor A","family":"Horton","sequence":"first","affiliation":[{"name":"Harvard Medical School Department of Biomedical Informatics, , Boston, MA 02115, USA"}]},{"given":"Burak H","family":"Alver","sequence":"additional","affiliation":[{"name":"Harvard Medical School Department of Biomedical Informatics, , Boston, MA 02115, USA"}]},{"given":"Peter J","family":"Park","sequence":"additional","affiliation":[{"name":"Harvard Medical School Department of Biomedical Informatics, , Boston, MA 02115, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,1,31]]},"reference":[{"key":"2023013111481024200_btaa048-B1","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1038\/35066075","article-title":"Chromosome territories, nuclear architecture and gene regulation in mammalian cells","volume":"2","author":"Cremer","year":"2001","journal-title":"Nat. Rev. Genet"},{"key":"2023013111481024200_btaa048-B2","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1038\/nature21711","article-title":"Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition","volume":"544","author":"Flyamer","year":"2017","journal-title":"Nature"},{"key":"2023013111481024200_btaa048-B3","volume-title":"Memorie di Metodologica Statistica","author":"Gini","year":"1912"},{"key":"2023013111481024200_btaa048-B4","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1038\/nmeth.2148","article-title":"Iterative correction of Hi-C data reveals hallmarks of chromosome organization","volume":"9","author":"Imakaev","year":"2012","journal-title":"Nat. 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Genet"},{"key":"2023013111481024200_btaa048-B8","article-title":"QuASAR: Quality Assessment of Spatial Arrangement Reproducibility in Hi-C Data","author":"Sauria","year":"2017","journal-title":"bioRxiv"},{"key":"2023013111481024200_btaa048-B9","doi-asserted-by":"crossref","DOI":"10.1093\/0198281935.001.0001","volume-title":"On Economic Inequality","author":"Sen","year":"1973"},{"key":"2023013111481024200_btaa048-B10","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature21429","article-title":"3D structures of individual mammalian genomes studied by single-cell Hi-C","volume":"544","author":"Stevens","year":"2017","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa048\/32471686\/btaa048.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/9\/2902\/48984510\/btaa048.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/9\/2902\/48984510\/btaa048.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T20:52:14Z","timestamp":1675198334000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/9\/2902\/5719021"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,1,31]]},"references-count":10,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2020,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa048","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,5,1]]},"published":{"date-parts":[[2020,1,31]]}}}