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About SpatialDM

SpatialDM (Spatial Direct Messaging, or Spatial co-expressed ligand and receptor Detected by Moran’s bivariant extension) is a statistical model and toolbox to identify the spatial co-expression (i.e., spatial association) between a pair of ligand and receptor.

Uniquely, SpatialDM can distinguish co-expressed ligand and receptor pairs from spatially separating pairs, and identify the spots of interaction.

With the analytical testing method, SpatialDM is scalable to 1 million spots within 12 min with only one core.

SpatialDM comprises two main steps:

1. global selection with spatialdm_global to identify significantly interacting LR pairs;

2. local selection with spatialdm_local to identify local spots for each interaction.

Please refer to our tutorials for details:

• Permutation-based SpatialDM (Recommended for small datasets, <10k spots).

• Differential analyses of whole interactome among varying conditions.

References

Li, Z., Wang, T., Liu, P., & Huang, Y. (2023). SpatialDM for rapid identification of spatially co-expressed ligand–receptor and revealing cell–cell communication patterns. Nature communications, 14(1), 3995. https://www.nature.com/articles/s41467-023-39608-w