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Several doublet detection algorithms are currently available, but their generalization performance could be further improved due to the lack of effective feature-embedding strategies with suitable model architectures. Therefore, SoCube, a novel deep learning algorithm, was developed to precisely detect doublets in various types of scRNA-seq data. SoCube (i) proposed a novel 3D composite feature-embedding strategy that embedded latent gene information and (ii) constructed a multikernel, multichannel CNN-ensembled architecture in conjunction with the feature-embedding strategy. With its excellent performance on benchmark evaluation and several downstream tasks, it is expected to be a powerful algorithm to detect and remove doublets in scRNA-seq data. SoCube is freely provided as an end-to-end tool on the Python official package site PyPi (https:\/\/pypi.org\/project\/socube\/) and open-source on GitHub (https:\/\/github.com\/idrblab\/socube\/).<\/jats:p>","DOI":"10.1093\/bib\/bbad104","type":"journal-article","created":{"date-parts":[[2023,3,20]],"date-time":"2023-03-20T15:57:46Z","timestamp":1679327866000},"source":"Crossref","is-referenced-by-count":10,"title":["SoCube: an innovative end-to-end doublet detection algorithm for analyzing scRNA-seq data"],"prefix":"10.1093","volume":"24","author":[{"given":"Hongning","family":"Zhang","sequence":"first","affiliation":[{"name":"Polytechnic Institute, The Second Affiliated Hospital, College of Pharmaceutical Sciences, Zhejiang University School of Medicine, Zhejiang University , Hangzhou 310058 , China"}]},{"given":"Mingkun","family":"Lu","sequence":"additional","affiliation":[{"name":"Polytechnic Institute, The Second Affiliated Hospital, College of Pharmaceutical Sciences, Zhejiang University School of Medicine, Zhejiang University , Hangzhou 310058 , China"}]},{"given":"Gaole","family":"Lin","sequence":"additional","affiliation":[{"name":"Polytechnic Institute, The Second Affiliated Hospital, College of Pharmaceutical Sciences, Zhejiang University School of Medicine, Zhejiang University , Hangzhou 310058 , China"}]},{"given":"Lingyan","family":"Zheng","sequence":"additional","affiliation":[{"name":"Polytechnic Institute, The Second Affiliated Hospital, College of Pharmaceutical Sciences, Zhejiang University School of Medicine, Zhejiang University , Hangzhou 310058 , China"}]},{"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Polytechnic Institute, The Second Affiliated Hospital, College of Pharmaceutical Sciences, Zhejiang University School of Medicine, Zhejiang University , Hangzhou 310058 , China"}]},{"given":"Zhijian","family":"Xu","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Materia Medica, Chinese 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