Squidpy: Spatial Transcriptomics

Squidpy is the scverse toolkit for spatially-resolved omics, built on AnnData and SpatialData. It answers questions a non-spatial scRNA-seq pipeline cannot: which cell types sit next to which (neighborhood enrichment), how cell-type pairs co-occur across distance (co-occurrence), which genes vary across tissue space (Moran's I / spatially variable genes), and what ligand-receptor signalling is plausible (ligrec). This skill does the spatial analysis; it hands non-spatial QC/clustering to alterlab-scanpy and spot deconvolution to alterlab-scvi-tools.

When to Use This Skill