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bio-tcr-bcr-analysis-scirpy-analysis

85 / 100 · Low risk

Fine to try.

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

Integrates single-cell paired TCR/BCR (10x VDJ, AIRR, dandelion, BD Rhapsody) with gene expression in an AnnData/MuData object using scirpy - chain-pairing QC, clonotype definition, clonal expansion, diversity, repertoire overlap, V(D)J usage, and VDJdb specificity. Operates on the awkward-array AIRR model (adata.obsm['airr'], accessed via get.airr after pp.index_chains), not legacy per-chain obs columns. Use when deciding clonotype definition for TCR (exact CDR3-nt identity via define_clonotyp…

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-tcr-bcr-analysis-scirpy-analysis' ] || [ -L ~/.agents/skills/'bio-tcr-bcr-analysis-scirpy-analysis' ]; then echo 'A skill folder named bio-tcr-bcr-analysis-scirpy-analysis 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-tcr-bcr-analysis-scirpy-analysis' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-tcr-bcr-analysis-scirpy-analysis' ~/.agents/skills/'bio-tcr-bcr-analysis-scirpy-analysis' && 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-tcr-bcr-analysis-scirpy-analysis' ~/.claude/skills/'bio-tcr-bcr-analysis-scirpy-analysis' (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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