Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

Nature Methods
Bo WangSerafim Batzoglou

Abstract

We present single-cell interpretation via multikernel learning (SIMLR), an analytic framework and software which learns a similarity measure from single-cell RNA-seq data in order to perform dimension reduction, clustering and visualization. On seven published data sets, we benchmark SIMLR against state-of-the-art methods. We show that SIMLR is scalable and greatly enhances clustering performance while improving the visualization and interpretability of single-cell sequencing data.

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Citations

Jan 25, 2018·Genes·Yuxuan YuanDavid Edwards
Oct 4, 2017·Nucleic Acids Research·Chieh LinZiv Bar-Joseph
Dec 22, 2017·Proteomics·Bo WangSerafim Batzoglou
May 5, 2018·Genome Research·Giovanni IaconoHolger Heyn
Feb 13, 2018·Bioinformatics·Seyoung Park, Hongyu Zhao
Nov 2, 2017·Briefings in Functional Genomics·Chung-Chau HonMichael J T Stubbington
Jul 31, 2018·The FEBS Journal·Helena Todorov, Yvan Saeys
Jan 20, 2018·Nature Communications·Davide RissoJean-Philippe Vert
Mar 5, 2019·PloS One·Gerard Martí-JuanUNKNOWN Alzheimer’s Disease Neuroimaging Initiative and the Alzheimer’s Disease Metabolomics Consortium
Mar 11, 2018·BMC Bioinformatics·Jesse M ZhangDavid N Tse
Apr 19, 2018·Nature Communications·Shahin MohammadiAnanth Grama
Dec 15, 2018·The FEBS Journal·Akshitkumar M MistryJonathan M Irish
Aug 29, 2018·Nature Biomedical Engineering·Holly M PolingMaxime M Mahe
Jun 28, 2019·Briefings in Bioinformatics·Raphael PetegrossoRui Kuang
Jul 28, 2019·Immunology·Candace C LiuAaron M Newman
Jan 19, 2018·Current Protocols in Cytometry·Kirsten E DigginsJonathan M Irish
Nov 30, 2019·Nucleic Acids Research·Ruth HuhYun Li
Dec 17, 2019·Science Advances·Divyansh Agarwal, Nancy R Zhang
Feb 20, 2020·Bioinformatics·Junlin XuJiaLiang Yang
Jun 22, 2019·Scientific Reports·Benjamin SzubertIgnat Drozdov
Sep 9, 2019·GigaScience·Luca AlessandrìRaffaele A Calogero
Jul 5, 2019·Briefings in Bioinformatics·Ren QiQuan Zou
Jul 24, 2020·Journal of Bioinformatics and Computational Biology·Hong-Dong LiJianxin Wang
Jun 28, 2020·Bioinformatics·Alessandra Cabassi, Paul D W Kirk

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