Fast-developing single-cell multimodal omics (scMulti-omics) technologies enable the measurement of multiple modalities, such as DNA methylation, chromatin accessibility, RNA expression, protein abundance, gene perturbation, and spatial information, from the same cell. scMulti-omics can comprehensively explore and identify cell characteristics, while also presenting challenges to the development of computational methods and tools for integrative analyses. Here, we review these integrative methods and summarize the existing tools for studying a variety of scMulti-omics data. The various functionalities and practical challenges in using the available tools in the public domain are explored through several case studies. Finally, we identify remaining challenges and future trends in scMulti-omics modeling and analyses.

快速发展的单细胞多模式组学 (scMulti-omics) 技术能够测量同一细胞的多种模式，例如 DNA 甲基化、染色质可及性、RNA 表达、蛋白质丰度、基因扰动和空间信息。 scMulti-omics可以全面探索和识别细胞特征，同时也对综合分析计算方法和工具的开发提出了挑战。在这里，我们回顾了这些综合方法，并总结了用于研究各种 scMulti-omics 数据的现有工具。通过几个案例研究探讨了使用公共领域可用工具的各种功能和实际挑战。最后，我们确定了 scMulti-omics 建模和分析中剩余的挑战和未来趋势。