ScDIFF: automatic cell type annotation using scATAC-seq data by incorporating bulk-level genomic and epigenomic information in a deep diffusive transformer.

ABSTRACT: Single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) provides an opportunity to look deeply into the gene regulation mechanism at the single-cell resolution. With the rapid accumulation of scATAC-seq data, there is an urgent need for automatic cell type annotations using scATAC-seq data. Most existing methods rely on creating artificial gene activity matrix, due to the extreme sparsity nature of the scATAC-seq data. However, these methods fail to exploit the intrinsic information inherent in the scATAC-seq peaks. We present scDIFF, a diffusive transformer-based method that integrates bulk-level genomic and epigenomic information with scATAC-seq data to annotate cell types without creating artificial gene activity matrix. Our scDIFF performed constantly better than

SUBMITTER: Wang HY 

PROVIDER: S-EPMC12616849 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature