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

TL;DR

This paper introduces ScNucAdapt, a novel partial domain adaptation method that enables accurate cross-domain cell type annotation between scRNA-seq and snRNA-seq datasets, addressing distributional and cell composition differences.

Contribution

The paper presents ScNucAdapt, the first method specifically designed for cross-annotation between paired and unpaired scRNA-seq and snRNA-seq datasets using partial domain adaptation.

Findings

Outperforms existing methods in cross-domain cell type annotation

Robust accuracy across paired and unpaired datasets

Effective handling of distributional differences

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, 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.