Individual skill

spatial-transcriptomics-cell-type-annotation

Spatial transcriptomics cell type annotation for single-cell-resolution platforms (Xenium, MERFISH, CosMx, SeqFISH): CELLxGENE reference download, Harmony label transfer, per-cluster marker evidence naming lineages then subtypes, spatial niches. Visium/Slide-seq spots: GPU -> spatial-transcriptomics-deconvolution-cell2location; CPU -> spatial-mapping-tangram (cell types: per-spot proportions); no reference -> spatial-domain-detection (regions: domains from markers). Beyond labels (microenvironment, arrangement, spatial patterns): read spatial-transcriptomics-analysis-squidpy before asking the user.

skills/genomics-bioinformatics/spatial-transcriptomics/spatial-transcriptomics-cell-type-annotation/SKILL.md

Source commit 55c1bd3e863d11bf5a853d24bcdda10c88e6eddf

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Last checked

Nov 5, 2026

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