FastIntegration: a fast and high-capacity version of Seurat Integration for large-scale integration of single-cell data

Abstract Atlas-scale integration of hundreds or even thousands of samples has become crucial for creating comprehensive cell maps. Here, we present FastIntegration which can integrate more than 4 million cells within 2 days. It outputs batch corrected values for all genes that we can use for downstream analyses. For the first time, we demonstrated that using batch corrected values can improve the performance of downstream analyses. In particular we demonstrated more accurately identified differentially expressed genes for cell types that are not shared between batches. Moreover, we also showed that FastIntegration outperforms existing methods for both homogeneous and heterogeneous data integration.