spatial-mapping-tangram
From the author
Tangram (tangram-sc) mapping of scRNA-seq onto spatial transcriptomics (Visium, Slide-seq, MERFISH, Xenium), one skill for every Tangram task: marker training genes, cells/clusters/constrained mode, per-spot cell type proportions, held-out gene validation (training scores, compare_spatial_geneexp, AUC, k-fold CV), imputation of unmeasured or dropout genes (project_genes; gimVI alternative), and Visium deconvolution into segmented nuclei with the tissue image (squidpy watershed, target_count, deconvolve_cell_annotations). Task-specific routes follow the main workflow. For probabilistic spot abundances with uncertainty use spatial-transcriptomics-deconvolution-cell2location.
Install
npx skills add jaechang-hits/SciAgent-Skills --skill spatial-mapping-tangram -a claude-code
Installs to .claude/skills/spatial-mapping-tangram/ · Each command fetches the skill straight from GitHub with the open skills CLI.
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