single-cell-rna-qc

SKILL.md

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.