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Research · Skill

Single-Cell RNA-seq Quality Control

Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis.

  • Ships scripts Phở cannot run yet
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What the skill covers

The sections of its instructions, in order.

  1. 01 When to Use This Skill
  2. 02 Approach 1: Complete QC Pipeline (Recommended for Standard Workflows)
  3. Workflow Steps
  4. 03 Approach 2: Modular Building Blocks (For Custom Workflows)
  5. 04 Best Practices
  6. 05 Reference Materials
  7. 06 Next Steps After QC

Reference files

4 files Phở can open while it uses the skill.

  • references/scverse_qc_guidelines.md
  • scripts/qc_analysis.py
  • scripts/qc_core.py
  • scripts/qc_plotting.py

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Frequently asked questions

What does Single-Cell RNA-seq Quality Control do?

Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis.

Is Single-Cell RNA-seq Quality Control free to use?

Yes. Single-Cell RNA-seq Quality Control is published by Anthropic under the Apache 2.0 licence, and you can use it with a free Phở account.

How do I use Single-Cell RNA-seq Quality Control in Phở?

Press Open in Phở, then Try to apply it to your next message, or add the Bio research set so Phở loads it whenever a request matches.

Does Single-Cell RNA-seq Quality Control need other tools?

No. It works in a normal Phở chat with what you type or upload. It also ships scripts, which Phở chat cannot run yet; Phở follows its written steps.

Copied unchanged from anthropics/knowledge-work-plugins at commit d900840 and credited to Anthropic, who is not affiliated with Phở. The full instructions and licence text ship with the skill inside Phở.