scFseCluster: A Feature Selection Enhanced Clustering for Single Cell RNA-seq Data

Single-cell RNA sequencing (scRNA-seq) enables researchers to reveal previously unknown cell heterogeneity and functional diversity, which is impossible with bulk RNA sequencing. Clustering approaches are widely used for analyzing scRNA-seq data and identifying cell types and states. In the past few years, various advanced computational strategies emerged. However, the low generalization and high computational cost are the main bottlenecks of existing methods. In this study, we established a novel computational framework, scFseCluster, for scRNA-seq clustering analysis. scFseCluster incorporates a metaheuristic algorithm FSQSSA to extract the optimal gene set, which largely guarantees the performance of cell clustering. We conducted simulation experiments in several aspects to verify the performance of the proposed approach. scFseCluster performed very well on six benchmark scRNA-seq datasets due to the optimal gene sets obtained using the FSQSSA algorithm. The comparative study demonstrated the significant advantages of scFseCluster over seven SOTA algorithms. In addition, our analysis shows that feature selection on high-variable genes (HVGs) can significantly improve clustering performance. In conclusion, our study demonstrates that scFseCluster is a highly versatile tool for enhancing scRNA-seq data clustering analysis.