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cell-type-annotation

100 / 100 · Low risk

Fine to try.

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

scRNA-seq cell type annotation - read before any annotation skills. Chooses and runs the route: name clusters manually from canonical markers (scanpy, runnable code here), transfer labels with CellTypist or a popV/scANVI on a reference, or do both and validate one against other. Covers package availability, tissue- and state-matched references, marker panels, confidence and marker validation of transferred labels, doublets, unresolved clusters. Tool-specific code lives in celltypist/popv-cell-a…

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/'cell-type-annotation' ] || [ -L ~/.agents/skills/'cell-type-annotation' ]; then echo 'A skill folder named cell-type-annotation 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 "$d" checkout --quiet '65d6ceb875e20b751ffb3a6d8ee19516558789e1' -- 'skills/genomics-bioinformatics/single-cell/cell-type-annotation' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/genomics-bioinformatics/single-cell/cell-type-annotation' ~/.agents/skills/'cell-type-annotation' && 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/'cell-type-annotation' ~/.claude/skills/'cell-type-annotation' (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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