Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data

F1000Research
Saskia FreytagMelanie Bahlo

Abstract

Background: The commercially available 10x Genomics protocol to generate droplet-based single-cell RNA-seq (scRNA-seq) data is enjoying growing popularity among researchers. Fundamental to the analysis of such scRNA-seq data is the ability to cluster similar or same cells into non-overlapping groups. Many competing methods have been proposed for this task, but there is currently little guidance with regards to which method to use. Methods: Here we use one gold standard 10x Genomics dataset, generated from the mixture of three cell lines, as well as three silver standard 10x Genomics datasets generated from peripheral blood mononuclear cells to examine not only the accuracy but also robustness of a dozen methods. Results: We found that some methods, including Seurat and Cell Ranger, outperform other methods, although performance seems to be dependent on the complexity of the studied system. Furthermore, we found that solutions produced by different methods have little in common with each other. Conclusions: In light of this, we conclude that the choice of clustering tool crucially determines interpretation of scRNA-seq data generated by 10x Genomics. Hence practitioners and consumers should remain vigilant about the outcome of 1...Continue Reading

Citations

Mar 14, 2019·Bioinformatics·Ghislain DurifFranck Picard
Jul 24, 2019·Journal of Bone and Mineral Research : the Official Journal of the American Society for Bone and Mineral Research·Matthew B GreenblattSarfaraz Lalani
Oct 28, 2018·BMC Genomics·Marmar Moussa, Ion I Măndoiu
Nov 29, 2019·Nucleic Acids Research·Ruth HuhYun Li
Jun 2, 2020·Nucleic Acids Research·Suluxan MohanrajTrevor J Pugh
Jun 22, 2019·Genome Biology·Lukas M WeberMark D Robinson
Nov 2, 2019·Briefings in Bioinformatics·Xinlei ZhaoJue Fan

Related Concepts

Research Personnel
RNA
Silver
Cell Line, Tumor
Advice
Peripheral Blood
Lipid Droplet
Single-Cell Analysis
Mononuclear Cells
RNA Analysis

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