SinNLRR: a robust subspace clustering method for cell type detection by non-negative and low-rank representation

Bioinformatics
Ruiqing ZhengJianxin Wang

Abstract

The development of single-cell RNA-sequencing (scRNA-seq) provides a new perspective to study biological problems at the single-cell level. One of the key issues in scRNA-seq analysis is to resolve the heterogeneity and diversity of cells, which is to cluster the cells into several groups. However, many existing clustering methods are designed to analyze bulk RNA-seq data, it is urgent to develop the new scRNA-seq clustering methods. Moreover, the high noise in scRNA-seq data also brings a lot of challenges to computational methods. In this study, we propose a novel scRNA-seq cell type detection method based on similarity learning, called SinNLRR. The method is motivated by the self-expression of the cells with the same group. Specifically, we impose the non-negative and low rank structure on the similarity matrix. We apply alternating direction method of multipliers to solve the optimization problem and propose an adaptive penalty selection method to avoid the sensitivity to the parameters. The learned similarity matrix could be incorporated with spectral clustering, t-distributed stochastic neighbor embedding for visualization and Laplace score for prioritizing gene markers. In contrast to other scRNA-seq clustering methods, ...Continue Reading

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Citations

Oct 1, 2019·Briefings in Bioinformatics·Pingjian DingChee-Keong Kwoh
Jul 24, 2020·Journal of Bioinformatics and Computational Biology·Hong-Dong LiJianxin Wang
Feb 23, 2020·Interdisciplinary Sciences, Computational Life Sciences·Xiaoshu ZhuHong-Dong Li
May 20, 2020·Frontiers in Genetics·Ruiqing ZhengMin Li
Aug 19, 2020·International Journal of Molecular Sciences·Zhenqiu Liu
Mar 2, 2021·Genomics, Proteomics & Bioinformatics·Zhenlan LiangJianxin Wang
Apr 7, 2021·Briefings in Bioinformatics·Xiangtao LiKa-Chun Wong
Jun 3, 2021·Interdisciplinary Sciences, Computational Life Sciences·Jin-Xing LiuSheng-Jun Li
Aug 27, 2021·BioMed Research International·Dong Yang, Xuchang Zhu
Sep 4, 2021·Bioinformatics·Bo YangYi-Jie Wang

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