single-cell-rna-qc

Runs QC on .h5ad and 10x .h5 single-cell files using scverse best practices, writing filtered matrices and QC plots.

Type	Claude Skill
Supplier	Anthropic
Availability	GA — first Anthropic-published scientific skill, released with Claude for Life Sciences (Oct 2025)
Pricing	Free / OSS
Capabilities	Read/Write

How to install

• Claude Code — plugin marketplace:

  /plugin marketplace add anthropics/life-sciences
  /plugin install single-cell-rna-qc@life-sciences
  

• Claude.ai — Settings → Capabilities → Skills → Upload skill, using the skill ZIP from the anthropics/life-sciences repo.

What it does

Skill instructions plus bundled scripts that perform MAD-based filtering on gene counts, total counts, and mitochondrial percentage, and emit standard QC visualizations.

Primary use cases: First-pass single-cell RNA-seq quality control, doublet / empty-droplet filtering, generating QC figures for downstream Scanpy / scvi-tools workflows.

Notes

Reads AnnData .h5ad or 10x Cell Ranger .h5. Uses median-absolute-deviation thresholds in line with scverse guidance. Auto-detects format.

Sources

• Skill source (SKILL.md)
• Anthropic tutorial
• Claude for Life Sciences announcement

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