From G1 to M: a comparative study of methods for identifying cell cycle phases

Abstract

Accurate identification of cell cycle phases in single-cell RNA-sequencing (scRNA-seq) data is crucial for biomedical research. Many methods have been developed to tackle this challenge, employing diverse approaches to predict cell cycle phases. In this review article, we delve into the standard processes in identifying cell cycle phases within scRNA-seq data and present several representative methods for comparison. To rigorously assess the accuracy of these methods, we propose an error function and employ multiple benchmarking datasets encompassing human and mouse data. Our evaluation results reveal a key finding: the fit between the reference data and the dataset being analyzed profoundly impacts the effectiveness of cell cycle phase identification methods. Therefore, researchers must carefully consider the compatibility between the reference data and their dataset to achieve optimal results. Furthermore, we explore the potential benefits of incorporating benchmarking data with multiple known cell cycle phases into the analysis. Merging such data with the target dataset shows promise in enhancing prediction accuracy. By shedding light on the accuracy and performance of cell cycle phase prediction methods across diverse datasets, this review aims to motivate and guide future methodological advancements. Our findings offer valuable insights for researchers seeking to improve their understanding of cellular dynamics through scRNA-seq analysis, ultimately fostering the development of more robust and widely applicable cell cycle identification methods.

Ploidy inference from single-cell data: application to human and mouse cell atlases

“…We introduced the S phase score to measure single-cell proliferation by comparing DNA copy numbers at the origins and termini of replication. Several algorithms exist for assigning cell cycle phases to single cells using scRNA-seq data ( Andrews et al 2021 ; Guo and Chen 2024 ). Our analysis is based on ATAC-seq and depicts the S phase without distinguishing between the G 2 , M and G 1 phases.…”