Bioinformatics. 2023 Nov 7:btad641. doi: 10.1093/bioinformatics/btad641. Online ahead of print.
ABSTRACT
MOTIVATION: The recent development of spatial resolved transcriptomics (SRT) technologies has facilitated research on gene expression in the spatial context. Annotating cell types is one crucial step for downstream analysis. However, many existing algorithms employ an unsupervised strategy to assign cell types for SRT data. They first conduct clustering analysis and then aggregate cluster-level expression based on the clustering results. This workflow fails to leverage the marker gene information efficiently. On the other hand, other cell annotation methods designed for single-cell RNA-seq (scRNA-seq) data utilize the cell-type marker genes information but fail to use spatial information in SRT data.
RESULTS: We introduce a statistical spatial transcriptomics cell assignment model, SPAN, to annotate clusters of cells or spots into known types in SRT data with prior knowledge of predefined marker genes and spatial information. The SPAN model annotates cells or spots from SRT data using predefined overexpressed marker genes and combines a mixture model with a hidden Markov random field to model the spatial dependency between neighboring spots. We demonstrate the effectiveness of SPAN against spatial and non-spatial clustering algorithms through extensive simulation and real data experiments.
AVAILABILITY: https://github.com/ChengZ352/SPAN.
PMID:37944045 | DOI:10.1093/bioinformatics/btad641
