RT Journal
A1 Liu, Qi
A1 Hsu, Chih-Yuan
A1 Shyr, Yu
T1 Scalable and model-free detection of spatial patterns and colocalization
JF Genome Research 
JO Genome Research 
YR 2022 
FD September 01 
VO 32 
IS 9 
SP 1736 
OP 1745 
DO 10.1101/gr.276851.122 
UL http://genome.cshlp.org/content/32/9/1736.abstract 
AB 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.