alterlab-squidpy-spatial

# 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 Use when the request involves: - Spatial transcriptomics / spatially-resolved omics on **Visium, Visium HD, Xenium, MERFISH/MERSCOPE, or CosMx** data. - Building a **spatial neighbor graph** and running **neighborhood enrichment**, **co-occurrence**, **interaction matrix**, **Ripley's statistics**, or **centrality scores**. - Finding **spatially variable genes** via Moran's I (`spatial_autocorr`) or Sepal. - **Ligand-receptor** analysis in a spatial context (`ligrec`). - Identifying **spatial niches / tissue domains** (`calculate_niche_*`: neighborhood profile, UTAG, CellCharter, SpatialLeiden). - Reading platform output into AnnData/SpatialData and choosing the right `coord_type` for the platform. ### Does NOT Trigger | Request | Route to | |---------|----------| | Non-spatial scRNA-seq QC, normalization, PCA/UMAP, Leiden clustering, marker ge...