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

Ruiqing ZhengJianxin Wang


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


Aug 17, 2002·Science·Michael B ElowitzPeter S Swain
Jan 4, 2008·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·John D CahoyBen A Barres
Oct 14, 2008·Nature Neuroscience·Michael C OldhamDaniel H Geschwind
Mar 6, 2010·Nature Protocols·Fuchou TangM Azim Surani
Oct 22, 2013·Nature Methods·Angela R WuStephen R Quake
Mar 8, 2014·Arteriosclerosis, Thrombosis, and Vascular Biology·Stephanie A PopsonChristopher C W Hughes
Nov 25, 2014·Nature Neuroscience·Dmitry UsoskinPatrik Ernfors
Jan 30, 2015·Nature Reviews. Genetics·Oliver StegleJohn C Marioni
Jun 11, 2015·Proceedings of the National Academy of Sciences of the United States of America·Spyros DarmanisStephen R Quake
Aug 22, 2015·Development·Paul BlakeleyKathy K Niakan
Nov 4, 2015·Genome Biology·Emma Pierson, Christopher Yau
Jan 5, 2016·Nature Neuroscience·Bosiljka TasicHongkui Zeng
Mar 26, 2016·Cell·Mubeen GoolamMagdalena Zernicka-Goetz
Apr 12, 2016·Nature Structural & Molecular Biology·Chao YuHeng-Yu Fan
May 15, 2016·Nucleic Acids Research·Zhicheng Ji, Hongkai Ji
Mar 28, 2017·Nature Methods·Vladimir Yu KiselevMartin Hemberg
Oct 4, 2017·Nucleic Acids Research·Chieh LinZiv Bar-Joseph
Oct 11, 2017·Nature Methods·Sara AibarStein Aerts
Oct 27, 2017·Nature·Orit Rozenblatt-RosenSarah A Teichmann
Jan 20, 2018·Nature Communications·Davide RissoJean-Philippe Vert
Jan 24, 2018·Nucleic Acids Research·Debajyoti SinhaDebarka Sengupta
Feb 13, 2018·Bioinformatics·Seyoung Park, Hongyu Zhao
Jul 20, 2018·F1000Research·Jonathan Ronen, Altuna Akalin
Mar 10, 2018·Nature Communications·Wei Vivian Li, Jingyi Jessica Li
May 12, 2018·Genome Biology·Daphne Tsoucas, Guo-Cheng Yuan
Feb 19, 2019·Briefings in Bioinformatics·Xingyi LiMin Li

❮ Previous
Next ❯


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

❮ Previous
Next ❯

Related Concepts

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.


Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.


Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.