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alterlab-squidpy-spatial

95 / 100 · Low risk

Fine to try.

By AlterLab-IEU/AlterLab-Academic-Skills (GitHub) · research · 87 stars · scanned at commit 3ab6d03

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 us…

Works with any agent that supports SKILL.md skills.

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What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'alterlab-squidpy-spatial' ] || [ -L ~/.agents/skills/'alterlab-squidpy-spatial' ]; then echo 'A skill folder named alterlab-squidpy-spatial already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/AlterLab-IEU/AlterLab-Academic-Skills' "$d" && git -C "$d" checkout --quiet '3ab6d034385ec4fedc3f6f4099292d4e91f60300' -- 'skills/bioinformatics/alterlab-squidpy-spatial' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bioinformatics/alterlab-squidpy-spatial' ~/.agents/skills/'alterlab-squidpy-spatial' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'alterlab-squidpy-spatial' ~/.claude/skills/'alterlab-squidpy-spatial' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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