Multi-omics single-cell data integration and regulatory inference with graph-linked embedding.

To unify the cell type annotations, neighbor-based label transfer was conducted using the integrated cell embeddings and we observed highly significant marker overlap (Fig. 3e , three-way Fisher’s exact test 40 , false discovery rate (FDR) < 5 × 10 −17 ) for 12 out of the 14 mapped cell types (Supplementary Figs. 8g–o and 9 and Methods ), indicating reliable alignment.

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