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bio-single-cell-cell-annotation

85 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c

Automated reference-based cell type annotation for single-cell RNA-seq using CellTypist, SingleR, Azimuth, scANVI, and scmap to transfer labels from a reference. Use when annotating cell types from a reference atlas or pretrained model, transferring labels onto a query, assessing prediction confidence and rejection, or triaging whether an unexpected cluster is a novel type versus a doublet, low-quality, or batch artifact.

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/'bio-single-cell-cell-annotation' ] || [ -L ~/.agents/skills/'bio-single-cell-cell-annotation' ]; then echo 'A skill folder named bio-single-cell-cell-annotation already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-single-cell-cell-annotation' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-single-cell-cell-annotation' ~/.agents/skills/'bio-single-cell-cell-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/'bio-single-cell-cell-annotation' ~/.claude/skills/'bio-single-cell-cell-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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