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Here, we show that the live cell pool can be highly enriched with undefined heterogeneous cells, i.e. \u2018ungated\u2019 cells, and that current semi-automated approaches ignore their modeling resulting in misclassified annotations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Result<\/jats:title>\n                    <jats:p>We introduce \u2018CyAnno\u2019, a novel semi-automated approach for deconvoluting the unlabeled cytometry dataset based on a machine learning framework utilizing manually gated training data that allows the integrative modeling of \u2018gated\u2019 cell types and the \u2018ungated\u2019 cells. By applying this framework on several CyTOF datasets, we demonstrated that including the \u2018ungated\u2019 cells can lead to a significant increase in the precision of the \u2018gated\u2019 cell types prediction. CyAnno can be used to identify even a single cell type, including rare cells, with higher efficacy than current state-of-the-art semi-automated approaches.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The CyAnno is available as a python script with a user-manual and sample dataset at https:\/\/github.com\/abbioinfo\/CyAnno.<\/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\/btab409","type":"journal-article","created":{"date-parts":[[2021,5,24]],"date-time":"2021-05-24T15:13:01Z","timestamp":1621869181000},"page":"4164-4171","source":"Crossref","is-referenced-by-count":26,"title":["<i>CyAnno<\/i>\n                    : a semi-automated approach for cell type annotation of mass cytometry datasets"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5682-0209","authenticated-orcid":false,"given":"Abhinav","family":"Kaushik","sequence":"first","affiliation":[{"name":"Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diane","family":"Dunham","sequence":"additional","affiliation":[{"name":"Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziyuan","family":"He","sequence":"additional","affiliation":[{"name":"Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monali","family":"Manohar","sequence":"additional","affiliation":[{"name":"Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manisha","family":"Desai","sequence":"additional","affiliation":[{"name":"Quantitative Sciences Unit, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kari C","family":"Nadeau","sequence":"additional","affiliation":[{"name":"Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3093-2568","authenticated-orcid":false,"given":"Sandra","family":"Andorf","sequence":"additional","affiliation":[{"name":"Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA"},{"name":"Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH 45229, USA"},{"name":"Divisions of Biomedical Informatics and Allergy & Immunology, Cincinnati Children\u2019s Hospital Medical Center , Cincinnati, OH 45229, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,5,25]]},"reference":[{"key":"2023051607093666300_btab409-B1","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1002\/cyto.a.23738","article-title":"Predicting cell populations in single cell mass cytometry data","volume":"95","author":"Abdelaal","year":"2019","journal-title":"Cytom. 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