SpatialQuery: scalable discovery and molecular characterization of multicellular motifs from spatial omics data (opens in new tab)

Spatially resolved single-cell technologies enable profiling of cells in situ, yet computational approaches that jointly discover multicellular spatial patterns and characterize their molecular programs remain limited. Here we introduce SpatialQuery, a framework that can both identify cellular motifs, i.e. recurrent multicellular co-localization patterns, and perform molecular analyses focused on the motifs. It uncovers genes modulated by spatial contexts through differential expression analy...