{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T23:14:02Z","timestamp":1771024442413,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2017,5,13]],"date-time":"2017-05-13T00:00:00Z","timestamp":1494633600000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG006841"],"award-info":[{"award-number":["R01HG006841"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG006282"],"award-info":[{"award-number":["R01HG006282"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Emerging single-cell technologies (e.g. single-cell ATAC-seq, DNase-seq or ChIP-seq) have made it possible to assay regulome of individual cells. Single-cell regulome data are highly sparse and discrete. Analyzing such data is challenging. User-friendly software tools are still lacking. We present SCRAT, a Single-Cell Regulome Analysis Toolbox with a graphical user interface, for studying cell heterogeneity using single-cell regulome data. SCRAT can be used to conveniently summarize regulatory activities according to different features (e.g. gene sets, transcription factor binding motif sites, etc.). Using these features, users can identify cell subpopulations in a heterogeneous biological sample, infer cell identities of each subpopulation, and discover distinguishing features such as gene sets and transcription factors that show different activities among subpopulations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SCRAT is freely available at https:\/\/zhiji.shinyapps.io\/scrat as an online web service and at https:\/\/github.com\/zji90\/SCRAT as an R package.<\/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\/btx315","type":"journal-article","created":{"date-parts":[[2017,5,11]],"date-time":"2017-05-11T13:58:43Z","timestamp":1494511123000},"page":"2930-2932","source":"Crossref","is-referenced-by-count":55,"title":["Single-cell regulome data analysis by SCRAT"],"prefix":"10.1093","volume":"33","author":[{"given":"Zhicheng","family":"Ji","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA"}]},{"given":"Weiqiang","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA"}]},{"given":"Hongkai","family":"Ji","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,5,12]]},"reference":[{"key":"2023020206410931300_btx315-B1","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position","volume":"10","author":"Buenrostro","year":"2013","journal-title":"Nat. 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Biotechnol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/18\/2930\/49040940\/bioinformatics_33_18_2930.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/18\/2930\/49040940\/bioinformatics_33_18_2930.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T06:41:38Z","timestamp":1675320098000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/18\/2930\/3823309"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,5,12]]},"references-count":9,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2017,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx315","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,9,15]]},"published":{"date-parts":[[2017,5,12]]}}}