Qc Single Cell
Description
--- description: Quality control and filtering for single-cell RNA-seq. Use when the user has an h5ad/h5/10x matrix and wants QC, cell filtering, doublet detection, or asks why their cell count dropped. argument-hint: [h5ad-file] allowed-tools: Read Grep Glob Bash(python3 *) --- Run QC on `$0`. Follow the `single-cell-atlas` skill. The parts that are usually got wrong: 1. **Use MAD-based thresholds, not fixed cutoffs.** A hard `n_genes > 200` throws away real cells in low-complexity tissue an
Installation
Installs to ~/.claude/commands/zamushwani-biomedical-ai-skills-qc-single-cell.md
mkdir -p ~/.claude/commands && curl -fsSL https://raw.githubusercontent.com/zamushwani/biomedical-ai-skills/HEAD/.claude/commands/qc-single-cell.md -o ~/.claude/commands/zamushwani-biomedical-ai-skills-qc-single-cell.md Restart Claude Code, or start a new session, for it to be picked up.
Full documentation available on GitHub
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