Seurat is the core single-cell genomics analysis toolkit in the R language ecosystem, developed and maintained by the Satija laboratory. The newly released Seurat v5 version introduces significant updates in spatial transcriptomics, multi-modal data integration, and large-scale single-cell data analysis, while maintaining backward compatibility with previous versions. Seurat provides a complete workflow from data quality control, standardization, dimension reduction, clustering to differential expression analysis and cell type annotation, and supports seamless integration with various integration algorithms such as Harmony and LIGER. Its rich visualization capabilities and active community ecosystem make it the de facto standard for single-cell transcriptome data analysis.