CellTypist (Claude Skill)

Automated scRNA-seq cell type annotation via pre-trained logistic regression.


Type	Claude Skill
Supplier	jaechang-hits (community OSS, CC BY 4.0)
Availability	GA — part of the BixBench-evaluated SciAgent-Skills collection
Pricing	Free / OSS (MIT)
Capabilities	Read/Write — Claude runs the skill’s Python locally (Bash), not as an MCP tool

How to install

SciAgent-Skills is not an npm package — skills are plain markdown read directly by the agent (no npx/npm).

Claude Code — clone and load as a plugin:
```
git clone https://github.com/jaechang-hits/SciAgent-Skills
```
Then inside Claude Code run /plugin install sciagent-skills (verify it appears under /plugin → Installed). Clone into your project directory so Claude Code picks the skills up via CLAUDE.md.
Manual / other agents — point the agent at the skill file directly:
```
cp -r SciAgent-Skills/skills/genomics-bioinformatics/single-cell/celltypist-cell-annotation ~/.claude/skills/
```
The skill declares its own Python dependencies in its SKILL.md; install them when prompted on first use.

What it does

Automated scRNA-seq cell type annotation via pre-trained logistic regression. 45+ models: immune, gut, lung, brain, fetal, cancer microenvironments. Input normalized AnnData; outputs per-cell labels, majority-vote cluster labels, confidence scores. Use for fast, reference-backed annotation without manual marker inspection.

Primary use cases: fast, reference-backed annotation without manual marker inspection.

Notes

Distributed as a SKILL.md (plus code examples) in the SciAgent-Skills collection — Claude executes it locally via Bash/Python rather than as an MCP server. Upstream license: MIT. The skill directory upstream is skills/genomics-bioinformatics/single-cell/celltypist-cell-annotation.

Sources

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