alterlab-squidpy-spatial

SKILLWorkflowcommunity
v0.0.0AlterLab-IEUMITUpdated 3mo agoSource →

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-

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3mo agoLast update
Skill
AuthorAlterLab-IEU
Version0.0.0
LicenseMIT
CategoryWorkflow
Formatsskill.md
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About

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_occurre

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