{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:58Z","timestamp":1772138098178,"version":"3.50.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2019,6,14]],"date-time":"2019-06-14T00:00:00Z","timestamp":1560470400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Australian National Health and Medical Research Council Program","award":["105461"],"award-info":[{"award-number":["105461"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Dropout is a common phenomenon in single-cell RNA-seq (scRNA-seq) data, and when left unaddressed it affects the validity of the statistical analyses. Despite this, few current methods for differential expression (DE) analysis of scRNA-seq data explicitly model the process that gives rise to the dropout events. We develop DECENT, a method for DE analysis of scRNA-seq data that explicitly and accurately models the molecule capture process in scRNA-seq experiments.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We show that DECENT demonstrates improved DE performance over existing DE methods that do not explicitly model dropout. This improvement is consistently observed across several public scRNA-seq datasets generated using different technological platforms. The gain in improvement is especially large when the capture process is overdispersed. DECENT maintains type I error well while achieving better sensitivity. Its performance without spike-ins is almost as good as when spike-ins are used to calibrate the capture model.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The method is implemented as a publicly available R package available from https:\/\/github.com\/cz-ye\/DECENT.<\/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\/btz453","type":"journal-article","created":{"date-parts":[[2019,6,6]],"date-time":"2019-06-06T07:11:17Z","timestamp":1559805077000},"page":"5155-5162","source":"Crossref","is-referenced-by-count":38,"title":["DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data"],"prefix":"10.1093","volume":"35","author":[{"given":"Chengzhong","family":"Ye","sequence":"first","affiliation":[{"name":"Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Parkville, VIC, Australia"},{"name":"Department of Medical Biology, The University of Melbourne , Parkville, VIC, Australia"},{"name":"School of Medicine, Tsinghua University, Haidian District , Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Terence P","family":"Speed","sequence":"additional","affiliation":[{"name":"Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Parkville, VIC, Australia"},{"name":"Department of Mathematics and Statistics, The University of Melbourne , Parkville, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Agus","family":"Salim","sequence":"additional","affiliation":[{"name":"Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Parkville, VIC, Australia"},{"name":"Department of Mathematics and Statistics, La Trobe University , Bundoora, VIC, Australia"},{"name":"Baker Heart and Diabetes Institute , Melbourne, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,6,14]]},"reference":[{"key":"2023013108375098500_btz453-B1","doi-asserted-by":"crossref","first-page":"584.","DOI":"10.1038\/nmeth.4263","article-title":"Scnorm: robust normalization of single-cell RNA-seq data","volume":"14","author":"Bacher","year":"2017","journal-title":"Nat. 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