Smmit: A pipeline for integrating multiple single-cell multi-omics samples

Multi-sample single-cell multi-omics datasets, which simultaneously measure multiple data modalities in the same cells across multiple samples, facilitate the study of gene expression, gene regulatory activities, and protein abundances on a population scale. We developed Smmit, a computational pipeline for integrating data both across samples and modalities. Compared to existing methods, Smmit more effectively removes batch effects while preserving relevant biological information, resulting in superior integration outcomes. Additionally, Smmit is more computationally efficient and builds upon existing computational methods, requiring minimal effort for implementation. While the focus of Smmit is not algorithmic innovation, it provides an empirically useful solution for analyzing multi-sample single-cell multi-omics data. Smmit is an R software package that is freely available on GitHub: https://github.com/zji90/Smmit.