{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T18:46:15Z","timestamp":1776451575787,"version":"3.51.2"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,10,14]],"date-time":"2024-10-14T00:00:00Z","timestamp":1728864000000},"content-version":"vor","delay-in-days":21,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100012331","name":"Flanders Innovation and Entrepreneurship","doi-asserted-by":"publisher","award":["HBC_2022.0673"],"award-info":[{"award-number":["HBC_2022.0673"]}],"id":[{"id":"10.13039\/100012331","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Stilla Technologies"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Digital polymerase chain reaction (dPCR) is a best-in-class molecular biology technique for the accurate and precise quantification of nucleic acids. The recent maturation of dPCR technology allows the quantification of up to thousands of targeted nucleic acids per instrument per day. A key step in the dPCR data analysis workflow is the classification of partitions into two classes based on their partition intensities: partitions either containing or lacking target nucleic acids of interest. Much effort has been invested in the design and tailoring of automated dPCR partition classification procedures, and such procedures will be increasingly important as the technology ventures into high-throughput applications. However, automated partition classification is not fail-safe, and evaluation of its accuracy is\u00a0highly advised. This accuracy evaluation is a manual endeavor and is becoming a bottleneck for high-throughput dPCR applications. Here, we introduce dipcensR, the first data-analysis procedure that automates the assessment of any linear partition classifier\u2019s partition classification accuracy, offering potentially substantial efficiency gains. dipcensR is based on a robustness evaluation of said partition classification and flags classifications with low robustness as needing review. Additionally, dipcensR\u2019s robustness analysis underpins (optional) automatic optimization of partition classification to achieve maximal robustness. A freely available R implementation supports dipcensR\u2019s use.<\/jats:p>","DOI":"10.1093\/bib\/bbae507","type":"journal-article","created":{"date-parts":[[2024,10,14]],"date-time":"2024-10-14T11:31:34Z","timestamp":1728905494000},"source":"Crossref","is-referenced-by-count":1,"title":["Digital PCR threshold robustness analysis and optimization using <i>dipcensR<\/i>"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9875-385X","authenticated-orcid":false,"given":"Matthijs","family":"Vynck","sequence":"first","affiliation":[{"name":"Digital PCR Center (DIGPCR), Ghent University , Ghent ,","place":["Belgium"]},{"name":"Department of Morphology , Imaging, Orthopaedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, , Ghent ,","place":["Belgium"]},{"name":"Ghent University , Imaging, Orthopaedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, , Ghent ,","place":["Belgium"]},{"name":"Cancer Research Institute Ghent, Ghent University , C. Heymanslaan 10, 9000 Ghent ,","place":["Belgium"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wim","family":"Trypsteen","sequence":"additional","affiliation":[{"name":"Digital PCR Center (DIGPCR), Ghent University , Ghent ,","place":["Belgium"]},{"name":"Cancer Research Institute Ghent, Ghent University , C. Heymanslaan 10, 9000 Ghent ,","place":["Belgium"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olivier","family":"Thas","sequence":"additional","affiliation":[{"name":"Digital PCR Center (DIGPCR), Ghent University , Ghent ,","place":["Belgium"]},{"name":"Department of Applied Mathematics , Computer Science and Statistics, , Ghent ,","place":["Belgium"]},{"name":"Krijgslaan 281 - S9, 9000 Ghent University , Computer Science and Statistics, , Ghent ,","place":["Belgium"]},{"name":"Data Science Institute, Hasselt University , Agoralaan Gebouw D, 3590 Hasselt ,","place":["Belgium"]},{"name":"National Institute for Applied Statistics Research Australia, University of Wollongong , Wollongong, NSW 2522 ,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jo","family":"Vandesompele","sequence":"additional","affiliation":[{"name":"Digital PCR Center (DIGPCR), Ghent University , Ghent ,","place":["Belgium"]},{"name":"Cancer Research Institute Ghent, Ghent University , C. Heymanslaan 10, 9000 Ghent ,","place":["Belgium"]},{"name":"Department of Biomolecular Sciences, Ghent University , C. Heymanslaan 10, 9000 Ghent ,","place":["Belgium"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2097-8439","authenticated-orcid":false,"given":"Ward","family":"De Spiegelaere","sequence":"additional","affiliation":[{"name":"Digital PCR Center (DIGPCR), Ghent University , Ghent ,","place":["Belgium"]},{"name":"Department of Morphology , Imaging, Orthopaedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, , Ghent ,","place":["Belgium"]},{"name":"Ghent University , Imaging, Orthopaedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, , Ghent ,","place":["Belgium"]},{"name":"Cancer Research Institute Ghent, Ghent University , C. Heymanslaan 10, 9000 Ghent ,","place":["Belgium"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,10,14]]},"reference":[{"key":"2024101411311754200_ref1","doi-asserted-by":"publisher","first-page":"1012","DOI":"10.1093\/clinchem\/hvaa125","article-title":"The digital MIQE guidelines update: minimum information for publication of quantitative digital PCR experiments for 2020","volume":"66","author":"Huggett","year":"2020","journal-title":"Clin Chem"},{"key":"2024101411311754200_ref2","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1373\/clinchem.2019.304048","article-title":"Digital PCR\u2014An emerging technology with broad applications in microbiology","volume":"66","author":"Salipante","year":"2020","journal-title":"Clin Chem"},{"key":"2024101411311754200_ref3","doi-asserted-by":"publisher","first-page":"114344","DOI":"10.1016\/j.bios.2022.114344","article-title":"Emerging digital PCR technology in precision 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