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scgpt

100 / 100 · Low risk

Fine to try.

By aipoch/open-science (GitHub) · research · 5,526 stars · scanned at commit c4ae79b

Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology. Use this skill when: (1) Producing cell embeddings from an AnnData for clustering/integration, (2) Zero-shot or fine-tuned cell-type annotation, (3) Gene-level representation for perturbation/GRN tasks. For probabilistic single-cell models (scVI etc.), use the scvi-tools library.

Works with any agent that supports SKILL.md skills.

What this skill can do

We found nothing in the files we read that matches our rules. That does not prove the skill is safe: see the limits of static scanning.

Install

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

if [ -e ~/.agents/skills/'scgpt' ] || [ -L ~/.agents/skills/'scgpt' ]; then echo 'A skill folder named scgpt already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/aipoch/open-science' "$d" && git -C "$d" checkout --quiet 'c4ae79ba6ca5c97dcb1fb27518acda85319d7115' -- 'resources/skills/scgpt' && mkdir -p ~/.agents/skills && cp -R "$d"/'resources/skills/scgpt' ~/.agents/skills/'scgpt' && 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/'scgpt' ~/.claude/skills/'scgpt' (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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