alterlab-squidpy-spatial
byalterlab-ieu· 90 skills
Analyzes spatial transcriptomics with squidpy (1.8.x) on AnnData and SpatialData objects, routing platforms correctly: Visium spots use spatial_neighbors(coord_type='grid') and pair with deconvolution, while Xenium/MERFISH single-cell data use coord_type='generic'/Delaunay neighbors and spatialdata-io readers (xenium, visium_hd, merscope). Runs sq.gr.spatial_neighbors, nhood_enrichment, co_occurrence, spatial_autocorr (Moran's I for spatially variable genes), ripley, and ligrec. Use when the user wants spatial transcriptomics, squidpy, Visium/Xenium/MERFISH analysis, neighborhood enrichment, co-occurrence, or spatially variable genes; QC/clustering uses alterlab-scanpy and spot deconvolution (destVI/Tangram) uses alterlab-scvi-tools. Part of the AlterLab Academic Skills suite.
How to install alterlab-squidpy-spatial?
alterlab-ieu/alterlab-academic-skills/alterlab-squidpy-spatial
$npx -y skills add alterlab-ieu/alterlab-academic-skills --skill alterlab-squidpy-spatialInstalls into the current project.
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Run `npx skills use "https://github.com/alterlab-ieu/alterlab-academic-skills" --skill "alterlab-ieu/alterlab-academic-skills/alterlab-squidpy-spatial"` and follow the generated skill instructions now. Read its complete output, redirecting it to a temporary file first if necessary. Resolve relative paths from the supporting-files directory it provides.
Use the skills in "https://github.com/alterlab-ieu/alterlab-academic-skills" that are relevant to the current task. Run `npx skills add "https://github.com/alterlab-ieu/alterlab-academic-skills"` and select the relevant skills, then follow their instructions.
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