scGPT (Claude Skill)

Applies the scGPT single-cell foundation model to annotate, integrate, and perturb single-cell data, driven as a Claude skill.

Type	Claude Skill
Supplier	Bo Wang Lab, University of Toronto
Availability	GA — Claude Science research skill
Pricing	Free / OSS (MIT; weights on Hugging Face/Drive)
Capabilities	Read/Write — local inference; writes embeddings, annotations, and predictions
Verified	works · 2026-07-20
Security	cleared · 2026-07-20 — provenance matches bowang-lab/scGPT, MIT, active, no advisories

How to install

• Claude Science — enable the built-in scGPT research skill (Anthropic-hosted; not published to the public anthropics/life-sciences marketplace).
• Run the model yourself — the upstream model is open source:

  git clone https://github.com/bowang-lab/scGPT
  

  Follow the repo README for environment setup and model weights.

What it does

Runs scGPT for zero-shot and fine-tuned single-cell tasks: cell-type annotation, batch integration, gene-network inference, and perturbation-response prediction on AnnData inputs. Local inference only; pretrained weights fetched from Hugging Face/Drive.

Primary use cases: Cell-type annotation, single-cell integration, perturbation prediction

Notes

Claude Science: Featured as a research skill in Anthropic’s Claude Science. Its inclusion there is an independent signal of quality and trustworthiness for life-science work.

Local (your compute); GPU recommended. Complements scvi-tools (VAE-based single-cell models).

Sources

• bowang-lab/scGPT
• Cui et al. 2024, Nature Methods
• Anthropic — Claude Science: Connectors and skills

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