Automatic cell type identification methods for single-cell RNA sequencing

Comput Struct Biotechnol J. 2021 Oct 20;19:5874-5887. doi: 10.1016/j.csbj.2021.10.027. eCollection 2021.


Single-cell RNA sequencing (scRNA-seq) has become a powerful tool for scientists of many research disciplines due to its ability to elucidate the heterogeneous and complex cell-type compositions of different tissues and cell populations. Traditional cell-type identification methods for scRNA-seq data analysis are time-consuming and knowledge-dependent for manual annotation. By contrast, automatic cell-type identification methods may have the advantages of being fast, accurate, and more user friendly. Here, we discuss and evaluate thirty-two published automatic methods for scRNA-seq data analysis in terms of their prediction accuracy, F1-score, unlabeling rate and running time. We highlight the advantages and disadvantages of these methods and provide recommendations of method choice depending on the available information. The challenges and future applications of these automatic methods are further discussed. In addition, we provide a free scRNA-seq data analysis package encompassing the discussed automatic methods to help the easy usage of them in real-world applications.

Keywords: Automatic identification; Cell type; Eager learning; Lazy learning; Marker learning; Single-cell RNA sequencing (scRNA-seq).

Publication types

  • Review