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.
Duke Scholars
Altmetric Attention Stats
Dimensions Citation Stats
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
APA
Chicago
ICMJE
MLA
NLM
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