{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:41Z","timestamp":1772138081001,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":280,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: A recent article identified an artifact in multiple single-cell RNA-seq (scRNA-seq) datasets generated by the Fluidigm C1 platform. Specifically, Leng et al. showed significantly increased gene expression in cells captured from sites with small or large plate output IDs. We refer to this artifact as an ordering effect (OE). Including OE genes in downstream analyses could lead to biased results. To address this problem, we developed a statistical method and software called OEFinder to identify a sorted list of OE genes. OEFinder is available as an R package along with user-friendly graphical interface implementations which allows users to check for potential artifacts in scRNA-seq data generated by the Fluidigm C1 platform.<\/jats:p>\n                  <jats:p>Availability and implementation: OEFinder is freely available at https:\/\/github.com\/lengning\/OEFinder<\/jats:p>\n                  <jats:p>Contact: \u00a0rstewart@morgridge.org or lengning1@gmail.com<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw004","type":"journal-article","created":{"date-parts":[[2016,2,14]],"date-time":"2016-02-14T20:09:07Z","timestamp":1455480547000},"page":"1408-1410","source":"Crossref","is-referenced-by-count":17,"title":["OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data"],"prefix":"10.1093","volume":"32","author":[{"given":"Ning","family":"Leng","sequence":"first","affiliation":[{"name":"1 Morgridge Institute for Research,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeea","family":"Choi","sequence":"additional","affiliation":[{"name":"2 Department of Statistics, University of Wisconsin and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li-Fang","family":"Chu","sequence":"additional","affiliation":[{"name":"1 Morgridge Institute for Research,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James A.","family":"Thomson","sequence":"additional","affiliation":[{"name":"1 Morgridge Institute for Research,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christina","family":"Kendziorski","sequence":"additional","affiliation":[{"name":"3 Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ron","family":"Stewart","sequence":"additional","affiliation":[{"name":"1 Morgridge Institute for Research,"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,1,6]]},"reference":[{"key":"2023020112230244600_btw004-B1","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol"},{"key":"2023020112230244600_btw004-B2","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1126\/science.1245316","article-title":"Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells","volume":"343","author":"Deng","year":"2014","journal-title":"Science"},{"key":"2023020112230244600_btw004-B3","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1038\/nmeth.3549","article-title":"Oscope: a pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq experiments","volume":"12","author":"Leng","year":"2015","journal-title":"Nat. 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