Single Cell Rna Qc

anthropics/knowledge-work-pluginsOfficial

Runs the standard scverse QC pipeline on single-cell RNA-seq data with MAD-based filtering and generates before/after visualizations. Works with both h5ad files and 10X h5 outputs. The convenience script handles the full workflow automatically, but you can also use the modular functions if you need different thresholds for cell subsets or want to skip filtering entirely. Default thresholds are intentionally permissive to avoid losing rare populations. Outputs include filtered h5ad files ready for downstream analysis plus PNG plots showing count depth, gene detection, and mitochondrial content. This is the boring foundation work you need to do before anything interesting happens, packaged so you don't have to remember the scanpy incantations.

skills.sh installs: 2.5K
GitHub stars: 35.3K
last updated: Aug 21, 2026

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Install

$ npx -y skills add anthropics/knowledge-work-plugins --skill single-cell-rna-qc --agent claude-code

Installs into .claude/skills of the current project.

Files

Single-Cell RNA-seq Quality Control

Automated QC workflow for single-cell RNA-seq data following scverse best practices.

When to Use This Skill

Use when users:

Request quality control or QC on single-cell RNA-seq data
Want to filter low-quality cells or assess data quality
Need QC visualizations or metrics
Ask to follow scverse/scanpy best practices
Request MAD-based filtering or outlier detection

Supported input formats:

.h5ad files (AnnData format from scanpy/Python workflows)
.h5 files (10X Genomics Cell Ranger output)

Default recommendation: Use Approach 1 (complete pipeline) unless the user has specific custom requirements or explicitly requests non-standard filtering logic.

Approach 1: Complete QC Pipeline (Recommended for Standard Workflows)

For standard QC following scverse best practices, use the convenience script scripts/qc_analysis.py:

python3 scripts/qc_analysis.py input.h5ad
# or for 10X Genomics .h5 files:
python3 scripts/qc_analysis.py raw_feature_bc_matrix.h5

The script automatically detects the file format and loads it appropriately.

SKILL.md on GitHub

Details

Repository: github.com/anthropics/knowledge-work-plugins
Category: Code Review & Quality
First seen: May 16, 2026