Experiments

Here are the codes for runing analysis in the CONCISE manuscript.

Code for experiments #

• Analysis of Visium breast cancer data
  • Negative control study (HKG-ligand pairs)
  • Negative control study (HKG-receptor pairs)
  • Spatial gene-gene co-expression analysis
  • Spatial ligand-receptor interaction inference
• Analysis of Stereo-seq mouse embryo data
  • Negative control study (HKG-ligand pairs)
  • Negative control study (HKG-receptor pairs)
  • Spatial gene-gene co-expression analysis
  • Spatial ligand-receptor interaction inference
• Analysis of MERFISH mouse intestinal inflammation data
  • Spatial ligand-receptor interaction inference from fibroblasts to immune cells
  • Spatial ligand-receptor interaction inference among fibroblast populations