Scalable and model-free detection of spatial patterns and colocalization

Qi Liu, Chih Yuan Hsu, Yu Shyr

Research output: Contribution to journalArticlepeer-review

8 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)1736-1745
Number of pages10
JournalGenome Research
Issue number9
Publication statusPublished - 2022 Sept

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)


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