ScInfeR: an efficient method for annotating cell types and sub-types in single-cell RNA-seq, ATAC-seq, and spatial omics.

ABSTRACT: Cell-type annotation remains a major challenge in single-cell and spatial omics analysis. Most existing methods rely on single-cell RNA sequencing (scRNA-seq) references or predefined marker sets. However, the scarcity of high-quality scRNA-seq references and marker sets makes relying on a single approach prone to bias and limits usability. Furthermore, available methods for cell-type annotation in single-cell ATAC-sequencing (scATAC-seq) and spatial transcriptomics datasets perform poorly. Here, we present ScInfeR, a graph-based cell-type annotation method that combines information from both scRNA-seq references and marker sets. By integrating these two data sources, ScInfeR can accurately annotate broad range of cell-types. It employs a hierarchical framework inspired by message-passing

SUBMITTER: Kumar Swain A 

PROVIDER: S-EPMC12140018 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature