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spatial-transcriptomics-deconvolution-cell2location

95 / 100 · Low risk

Fine to try. Some of what it can do is expected: a coding skill usually runs build and test commands.

By jaechang-hits/SciAgent-Skills (GitHub) · coding · 388 stars · scanned at commit 65d6ceb

Visium and other spot-based spatial transcriptomics (Slide-seq, ST) cell type deconvolution with cell2location: load Space Ranger output, get a tissue-matched scRNA-seq reference from CELLxGENE, learn cell type signatures, estimate cell type abundance per spot with posterior uncertainty, and check the maps against marker genes. Default route for 'annotate cell types' on Visium when a GPU is available. Limits: needs a tissue- and state-matched reference; the default 30000 epochs take hours on CP…

Works with any agent that supports SKILL.md skills.

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/'spatial-transcriptomics-deconvolution-cell2location' ] || [ -L ~/.agents/skills/'spatial-transcriptomics-deconvolution-cell2location' ]; then echo 'A skill folder named spatial-transcriptomics-deconvolution-cell2location already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/jaechang-hits/SciAgent-Skills' "$d" && git -C "$d" checkout --quiet '65d6ceb875e20b751ffb3a6d8ee19516558789e1' -- 'skills/genomics-bioinformatics/spatial-transcriptomics/spatial-transcriptomics-deconvolution-cell2location' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/genomics-bioinformatics/spatial-transcriptomics/spatial-transcriptomics-deconvolution-cell2location' ~/.agents/skills/'spatial-transcriptomics-deconvolution-cell2location' && 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/'spatial-transcriptomics-deconvolution-cell2location' ~/.claude/skills/'spatial-transcriptomics-deconvolution-cell2location' (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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