{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T12:40:24Z","timestamp":1776170424633,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,27]],"date-time":"2022-12-27T00:00:00Z","timestamp":1672099200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFF1200902"],"award-info":[{"award-number":["2021YFF1200902"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["62203236"],"award-info":[{"award-number":["62203236"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["62273194"],"award-info":[{"award-number":["62273194"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["61873141"],"award-info":[{"award-number":["61873141"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["61721003"],"award-info":[{"award-number":["61721003"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Recent innovations in single-cell chromatin accessibility sequencing (scCAS) have revolutionized the characterization of epigenomic heterogeneity. Estimation of the number of cell types is a crucial step for downstream analyses and biological implications. However, efforts to perform estimation specifically for scCAS data are limited. Here, we propose ASTER, an ensemble learning-based tool for accurately estimating the number of cell types in scCAS data. ASTER outperformed baseline methods in systematic evaluation on 27 datasets of various protocols, sizes, numbers of cell types, degrees of cell-type imbalance, cell states and qualities, providing valuable guidance for scCAS data analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ASTER along with detailed documentation is freely accessible at https:\/\/aster.readthedocs.io\/ under the MIT License. It can be seamlessly integrated into existing scCAS analysis workflows. The source code is available at https:\/\/github.com\/biox-nku\/aster.<\/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\/btac842","type":"journal-article","created":{"date-parts":[[2022,12,26]],"date-time":"2022-12-26T14:33:53Z","timestamp":1672065233000},"source":"Crossref","is-referenced-by-count":17,"title":["ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility data"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3503-9306","authenticated-orcid":false,"given":"Shengquan","family":"Chen","sequence":"first","affiliation":[{"name":"School of Mathematical Sciences and LPMC, Nankai University , Tianjin 300071, China"}]},{"given":"Rongxiang","family":"Wang","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Beijing 100084, China"}]},{"given":"Wenxin","family":"Long","sequence":"additional","affiliation":[{"name":"School of Mathematical Sciences and LPMC, Nankai University , Tianjin 300071, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7533-3753","authenticated-orcid":false,"given":"Rui","family":"Jiang","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Beijing 100084, China"}]}],"member":"286","published-online":{"date-parts":[[2022,12,27]]},"reference":[{"key":"2023010801254859100_btac842-B1","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1186\/s13059-019-1854-5","article-title":"Assessment of computational methods for the analysis of single-cell ATAC-seq data","volume":"20","author":"Chen","year":"2019","journal-title":"Genome Biol"},{"key":"2023010801254859100_btac842-B2","doi-asserted-by":"crossref","first-page":"2177","DOI":"10.1038\/s41467-021-22495-4","article-title":"RA3 is a reference-guided approach for epigenetic characterization of single cells","volume":"12","author":"Chen","year":"2021","journal-title":"Nat. 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