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alterlab-cellxgene

80 / 100 · Low risk

Fine to try.

By AlterLab-IEU/AlterLab-Academic-Skills (GitHub) · research · 87 stars · scanned at commit 3ab6d03

Query the CZ CELLxGENE Census (200M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnData. Use when pulling reference single-cell RNA-seq data from the largest curated public atlas, running population-scale queries, or benchmarking your data against a reference — for analyzing your own dataset use scanpy or scvi-tools. Part of the AlterLab Academic Skills suite.

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/'alterlab-cellxgene' ] || [ -L ~/.agents/skills/'alterlab-cellxgene' ]; then echo 'A skill folder named alterlab-cellxgene already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/AlterLab-IEU/AlterLab-Academic-Skills' "$d" && git -C "$d" checkout --quiet '3ab6d034385ec4fedc3f6f4099292d4e91f60300' -- 'skills/bioinformatics/alterlab-cellxgene' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bioinformatics/alterlab-cellxgene' ~/.agents/skills/'alterlab-cellxgene' && 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/'alterlab-cellxgene' ~/.claude/skills/'alterlab-cellxgene' (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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