Partial domain adaptation enables cross domain cell type annotation between scRNA-seq and snRNA-seq

Abstract: Accurate cell type annotation across datasets is a key challenge in single-cell analysis. snRNA-seq enables profiling of frozen or difficult-to-dissociate tissues, complementing scRNA-seq by capturing fragile or rare cell types. However, cross-annotation between these two datasets remains largely unexplored, as existing methods treat them independently. We introduce ScNucAdapt, the first method designed for cross-annotation between scRNA-seq and snRNA-seq datasets. To address distributional and cell composition differences, ScNucAdapt employs partial domain adaptation. Experiments across diverse samples show that ScNucAdapt achieves robust and accurate cell type annotation, outperforming existing approaches. Therefore, ScNucAdapt provides a practical framework for the cross-domain cell type annotation between scRNA-seq and snRNA-seq data.