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Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering.

Publication ,  Journal Article
Fang, J; Chan, C; Owzar, K; Wang, L; Qin, D; Li, Q-J; Xie, J
Published in: Genome Biol
December 27, 2022

Most single-cell RNA sequencing (scRNA-seq) analyses begin with cell clustering; thus, the clustering accuracy considerably impacts the validity of downstream analyses. In contrast with the abundance of clustering methods, the tools to assess the clustering accuracy are limited. We propose a new Clustering Deviation Index (CDI) that measures the deviation of any clustering label set from the observed single-cell data. We conduct in silico and experimental scRNA-seq studies to show that CDI can select the optimal clustering label set. As a result, CDI also informs the optimal tuning parameters for any given clustering method and the correct number of cluster components.

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Published In

Genome Biol

DOI

EISSN

1474-760X

Publication Date

December 27, 2022

Volume

23

Issue

1

Start / End Page

269

Location

England

Related Subject Headings

  • Single-Cell Gene Expression Analysis
  • Single-Cell Analysis
  • Sequence Analysis, RNA
  • Gene Expression Profiling
  • Cluster Analysis
  • Bioinformatics
  • Algorithms
  • 08 Information and Computing Sciences
  • 06 Biological Sciences
  • 05 Environmental Sciences
 

Citation

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Fang, J., Chan, C., Owzar, K., Wang, L., Qin, D., Li, Q.-J., & Xie, J. (2022). Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering. Genome Biol, 23(1), 269. https://doi.org/10.1186/s13059-022-02825-5
Fang, Jiyuan, Cliburn Chan, Kouros Owzar, Liuyang Wang, Diyuan Qin, Qi-Jing Li, and Jichun Xie. “Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering.Genome Biol 23, no. 1 (December 27, 2022): 269. https://doi.org/10.1186/s13059-022-02825-5.
Fang J, Chan C, Owzar K, Wang L, Qin D, Li Q-J, et al. Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering. Genome Biol. 2022 Dec 27;23(1):269.
Fang, Jiyuan, et al. “Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering.Genome Biol, vol. 23, no. 1, Dec. 2022, p. 269. Pubmed, doi:10.1186/s13059-022-02825-5.
Fang J, Chan C, Owzar K, Wang L, Qin D, Li Q-J, Xie J. Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering. Genome Biol. 2022 Dec 27;23(1):269.

Published In

Genome Biol

DOI

EISSN

1474-760X

Publication Date

December 27, 2022

Volume

23

Issue

1

Start / End Page

269

Location

England

Related Subject Headings

  • Single-Cell Gene Expression Analysis
  • Single-Cell Analysis
  • Sequence Analysis, RNA
  • Gene Expression Profiling
  • Cluster Analysis
  • Bioinformatics
  • Algorithms
  • 08 Information and Computing Sciences
  • 06 Biological Sciences
  • 05 Environmental Sciences