{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T01:43:52Z","timestamp":1775526232262,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2018,11,8]],"date-time":"2018-11-08T00:00:00Z","timestamp":1541635200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Operational Infrastructure Support Program and Australian Government NHMRC IRIIS"},{"name":"NHMRC Senior Research Fellowship","award":["110297"],"award-info":[{"award-number":["110297"]}]},{"name":"NHMRC Program Grant","award":["1054618"],"award-info":[{"award-number":["1054618"]}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS-1646108"],"award-info":[{"award-number":["DMS-1646108"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Cell type composition of tissues is important in many biological processes. To help understand cell type composition using gene expression data, methods of estimating (deconvolving) cell type proportions have been developed. Such estimates are often used to adjust for confounding effects of cell type in differential expression analysis (DEA).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose dtangle, a new cell type deconvolution method. dtangle works on a range of DNA microarray and bulk RNA-seq platforms. It estimates cell type proportions using publicly available, often cross-platform, reference data. We evaluate dtangle on 11 benchmark datasets showing that dtangle is competitive with published deconvolution methods, is robust to outliers and selection of tuning parameters, and is fast. As a case study, we investigate the human immune response to Lyme disease. dtangle\u2019s estimates reveal a temporal trend consistent with previous findings and are important covariates for DEA across disease status.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>dtangle is on CRAN (cran.r-project.org\/package=dtangle) or github (dtangle.github.io).<\/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\/bty926","type":"journal-article","created":{"date-parts":[[2018,11,6]],"date-time":"2018-11-06T15:12:19Z","timestamp":1541517139000},"page":"2093-2099","source":"Crossref","is-referenced-by-count":141,"title":["dtangle: accurate and robust cell type deconvolution"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7794-8404","authenticated-orcid":false,"given":"Gregory J","family":"Hunt","sequence":"first","affiliation":[{"name":"Department of Statistics, University of Michigan, Ann Arbor, MI, USA"}]},{"given":"Saskia","family":"Freytag","sequence":"additional","affiliation":[{"name":"Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia"},{"name":"Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia"}]},{"given":"Melanie","family":"Bahlo","sequence":"additional","affiliation":[{"name":"Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia"},{"name":"Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia"}]},{"given":"Johann A","family":"Gagnon-Bartsch","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Michigan, Ann Arbor, MI, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,11,8]]},"reference":[{"key":"2023012810014799000_bty926-B1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0006098","article-title":"Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus","volume":"4","author":"Abbas","year":"2009","journal-title":"PLoS One"},{"key":"2023012810014799000_bty926-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/msb.134947","article-title":"Digital cell quantification identifies global immune cell dynamics during influenza infection","volume":"10","author":"Altboum","year":"2014","journal-title":"Mol. 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