{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T14:45:51Z","timestamp":1776437151113,"version":"3.51.2"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,9,6]],"date-time":"2019-09-06T00:00:00Z","timestamp":1567728000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Fundamental Research Funds for the Central Universities in China"},{"DOI":"10.13039\/501100008865","name":"Xiamen University","doi-asserted-by":"publisher","award":["20720170076"],"award-info":[{"award-number":["20720170076"]}],"id":[{"id":"10.13039\/501100008865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008865","name":"Xiamen University","doi-asserted-by":"publisher","award":["20720190106"],"award-info":[{"award-number":["20720190106"]}],"id":[{"id":"10.13039\/501100008865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61802323"],"award-info":[{"award-number":["61802323"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31801268"],"award-info":[{"award-number":["31801268"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61573296"],"award-info":[{"award-number":["61573296"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Alternative polyadenylation (APA) plays a key post-transcriptional regulatory role in mRNA stability and functions in eukaryotes. Single cell RNA-seq (scRNA-seq) is a powerful tool to discover cellular heterogeneity at gene expression level. Given 3\u2032 enriched strategy in library construction, the most commonly used scRNA-seq protocol\u201410\u00d7 Genomics enables us to improve the study resolution of APA to the single cell level. However, currently there is no computational tool available for investigating APA profiles from scRNA-seq data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present a package scDAPA for detecting and visualizing dynamic APA from scRNA-seq data. Taking bam\/sam files and cell cluster labels as inputs, scDAPA detects APA dynamics using a histogram-based method and the Wilcoxon rank-sum test, and visualizes candidate genes with dynamic APA. Benchmarking results demonstrated that scDAPA can effectively identify genes with dynamic APA among different cell groups from scRNA-seq data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The scDAPA package is implemented in Shell and R, and is freely available at https:\/\/scdapa.sourceforge.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\/btz701","type":"journal-article","created":{"date-parts":[[2019,9,4]],"date-time":"2019-09-04T19:28:55Z","timestamp":1567625335000},"page":"1262-1264","source":"Crossref","is-referenced-by-count":33,"title":["scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4803-2098","authenticated-orcid":false,"given":"Congting","family":"Ye","sequence":"first","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University , Xiamen, Fujian 361102, China"}]},{"given":"Qian","family":"Zhou","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University , Xiamen, Fujian 361102, China"}]},{"given":"Xiaohui","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University , Xiamen, Fujian 361005, China"},{"name":"National Institute for Data Science in Health and Medicine, Xiamen University , Xiamen, Fujian 361102, China"}]},{"given":"Chen","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Duke University , Durham, NC 27710, USA"}]},{"given":"Guoli","family":"Ji","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University , Xiamen, Fujian 361005, China"},{"name":"National Institute for Data Science in Health and Medicine, Xiamen University , Xiamen, Fujian 361102, China"}]},{"given":"Daniel R","family":"Saban","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Duke University , Durham, NC 27710, USA"},{"name":"Department of Immunology, Duke University , Durham, NC 27710, USA"}]},{"given":"Qingshun Q","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University , Xiamen, Fujian 361102, China"},{"name":"Graduate College of Biomedical Sciences, Western University of Health Sciences , Pomona, CA 91766, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,9,6]]},"reference":[{"key":"2023013110163638300_btz701-B1","doi-asserted-by":"crossref","first-page":"589.","DOI":"10.3389\/fpls.2019.00589","article-title":"Root hair single cell type specific profiles of gene expression and alternative polyadenylation under cadmium stress","volume":"10","author":"Cao","year":"2019","journal-title":"Front. Plant Sci"},{"key":"2023013110163638300_btz701-B2","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1016\/j.gpb.2017.06.001","article-title":"Alternative polyadenylation: methods, findings, and impacts","volume":"15","author":"Chen","year":"2017","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2023013110163638300_btz701-B3","doi-asserted-by":"crossref","first-page":"1334","DOI":"10.1016\/j.neuron.2017.08.024","article-title":"cTag-PAPERCLIP reveals alternative polyadenylation promotes cell-type specific protein diversity and shifts Araf isoforms with microglia activation","volume":"95","author":"Hwang","year":"2017","journal-title":"Neuron"},{"key":"2023013110163638300_btz701-B4","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/j.immuni.2019.02.007","article-title":"Microglial function is distinct in different anatomical locations during retinal homeostasis and degeneration","volume":"50","author":"O\u2019Koren","year":"2019","journal-title":"Immunity"},{"key":"2023013110163638300_btz701-B5","doi-asserted-by":"crossref","first-page":"176.","DOI":"10.3389\/fncel.2018.00176","article-title":"Microglia activation and immunomodulatory therapies for retinal degenerations","volume":"12","author":"Rashid","year":"2018","journal-title":"Front. 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