single-cell-rna-qc

SKILL.md

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

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

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

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: anthropics/life-sciences.

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