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, a method designed for cross-annotation between paired and unpaired scRNA-seq and snRNA-seq datasets. To address distributional and cell composition differences, ScNucAdapt employs partial domain adaptation. Experiments across both unpaired and paired scRNA-seq and snRNA-seq 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.
@article{arxiv.2511.08996,
title = {Partial domain adaptation enables cross domain cell type annotation between scRNA-seq and snRNA-seq},
author = {Xiran Chen and Quan Zou and Qinyu Cai and Xiaofeng Chen and Weikai Li and Yansu Wang},
journal= {arXiv preprint arXiv:2511.08996},
year = {2026}
}