Comprehensive Integration of Single-Cell Data
This paper presents the Seurat v3 framework for integrating single-cell datasets across different technologies, conditions, and modalities. It introduces 'anchors' — pairs of cells in a shared low-dimensional space representing a common biological state — to harmonize datasets and transfer labels. The methods enable joint analysis of scRNA-seq with other measurements such as protein (CITE-seq), chromatin accessibility, and spatial data.