---
title: "Single-Cell RNA-seq Quality Control"
type: skill
id: "knowledge-work-plugins/bio-research/single-cell-rna-qc"
category: "Research"
publisher: "Anthropic"
license: "Apache-2.0"
source: "https://github.com/anthropics/knowledge-work-plugins/tree/d900840"
canonical: "https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/single-cell-rna-qc"
open_in_pho: "https://pho.chat/customize?item=knowledge-work-plugins%2Fbio-research%2Fsingle-cell-rna-qc&utm_source=labs&utm_medium=skill-page&utm_campaign=skills-library"
---

# 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.

Source: Anthropic (Apache 2.0), copied at a pinned commit. Free to use. Part of the Phở Skills library (https://labs.pho.chat/en/skills).
Skill set: Bio research (https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research.md).

## What it covers
- When to Use This Skill
- Approach 1: Complete QC Pipeline (Recommended for Standard Workflows)
  - Workflow Steps
- Approach 2: Modular Building Blocks (For Custom Workflows)
- Best Practices
- Reference Materials
- Next Steps After QC

## Other skills in this set
- [Instrument Data to Allotrope Converter](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/instrument-data-to-allotrope.md): Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data…
- [nf-core Pipeline Deployment](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/nextflow-development.md): Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers…
- [Scientific Problem Selection Skills](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/scientific-problem-selection.md): This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users…
- [scvi-tools Deep Learning Skill](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/scvi-tools.md): Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3)…
- [Bio-Research Start](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/start.md): Set up your bio-research environment and explore available tools. Use when first getting oriented with the plugin, checking which literature, drug-discovery, or visualization MCP servers are…

## Use it
- In Phở: open https://pho.chat/customize?item=knowledge-work-plugins%2Fbio-research%2Fsingle-cell-rna-qc&utm_source=labs&utm_medium=skill-page&utm_campaign=skills-library and press Try, or add it so Phở loads it whenever a request matches. Phở works with your own API key (OpenAI, Anthropic, Google and others).
- Full instructions (original SKILL.md, unchanged): https://labs.pho.chat/skills/raw/knowledge-work-plugins/bio-research/skills/single-cell-rna-qc/SKILL.md
- Original files: https://github.com/anthropics/knowledge-work-plugins/tree/d900840 (Apache 2.0).
- Full machine-readable index: https://labs.pho.chat/skills.json