Scalable and model-free detection of spatial patterns and colocalization

The expeditious growth in spatial omics technologies enables the profiling of genome-wide molecular events at molecular and single-cell resolution, highlighting a need for fast and reliable methods to characterize spatial patterns. We developed SpaGene, a model-free method to discover spatial patterns rapidly in large-scale spatial omics studies. Analyzing simulation and a variety of spatially resolved transcriptomics data showed that SpaGene is more powerful and scalable than existing methods. Spatial expression patterns identified by SpaGene reconstruct unobserved tissue structures. SpaGene also successfully discovers ligand-receptor interactions through their colocalization.

Automated summary

The rapid growth of spatial omics technologies enables the profiling of genome-wide molecular events at molecular and single-cell resolution. SpaGene, a model-free method, is developed to discover spatial patterns rapidly in large-scale spatial omics studies. It outperforms existing methods in power and scalability, and is able to reconstruct unobserved tissue structures and discover ligand-receptor interactions through colocalization.