Comparative study on differential expression analysis methods for single-cell RNA sequencing data with small biological replicates: Based on single-cell transcriptional data of PBMCs from COVID-19 severe patients

Single-cell RNA sequencing (scRNA-seq) is a high-throughput experimental technique for studying gene expression at the single-cell level. As a key component of single-cell data analysis, differential expression analysis (DEA) serves as the foundation for all subsequent secondary studies. Despite the fact that biological replicates are of vital importance in DEA process, small biological replication is still common in sequencing experiment now, which may impose problems to current DEA methods. Therefore, it is necessary to conduct a thorough comparison of various DEA approaches under small biological replications. Here, we compare 6 performance metrics on both simulated and real scRNA-seq datasets to assess the adaptability of 8 DEA approaches, with a particular emphasis on how well they function under small biological replications. Our findings suggest that DEA algorithms extended from bulk RNA-seq are still competitive under small biological replicate conditions, whereas the newly developed method DEF-scRNA-seq which is based on information entropy offers significant advantages. Our research not only provides appropriate suggestions for selecting DEA methods under different conditions, but also emphasizes the application value of machine learning algorithms in this field.