spatial-transcriptomics-cell-cell-communication
From the author
Spatial cell-cell communication / ligand-receptor (LR) interaction analysis, one skill for every route: LIANA consensus ranking between annotated cell types, CellPhoneDB v5 permutation p-values, DEG method and spatial microenvironments, squidpy neighbourhood enrichment to keep spatially adjacent sender-receiver pairs, LIANA bivariate local LR scores on the tissue (works on Visium spots without labels), pathway-focused candidate evidence tables (immune checkpoints, chemokines, Notch, Wnt, TGF-beta) with contact vs secreted classes and PubMed co-mentions, and multi-sample Tensor-cell2cell and MISTy models. Xenium/MERFISH/CosMx cells, Visium spots, scRNA-seq. Route-specific steps follow the main workflow. Needs cell type labels first (spatial-transcriptomics-cell-type-annotation or a deconvolution skill).
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npx skills add jaechang-hits/SciAgent-Skills --skill spatial-transcriptomics-cell-cell-communication -a claude-code
Installs to .claude/skills/spatial-transcriptomics-cell-cell-communication/ · Each command fetches the skill straight from GitHub with the open skills CLI.
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Similar skills
Closest to this one by what they do and when they are used.
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