# Scrna Qc

> Execute the MAD-based single-cell RNA-seq QC workflow (scripts + Python API) to filter low-quality cells and emit reports plus filtered AnnData files.

- Skill: `majiayu000/scrna-qc` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds add majiayu000/scrna-qc`
- Raw SKILL.md: https://api.skillmd.com/api/skills/majiayu000/scrna-qc/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Integrations & APIs
- Author: majiayu000 (https://skillmd.com/u/majiayu000)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/majiayu000/scrna-qc

---


## At-a-Glance
- **description (10-20 chars):** QC autopilot
- **keywords:** scRNAseq, MAD, h5ad, QC, plots
- **measurable_outcome:** Produce filtered `.h5ad` files, before/after plots, and `qc_summary.json` within 20 minutes per dataset.

## Workflow
1. Accept `.h5ad`, 10x `.h5`, or 10x directory inputs; set mitochondrial/ribosomal patterns as needed.
2. Run `qc_analysis.py` (CLI) or call `qc_core` helpers to compute metrics, apply MAD thresholds, and filter cells/genes.
3. Generate standard plots (metrics before/after, threshold overlays) plus filtered data artifacts.
4. Document parameters (mad_counts/genes/mt, mt_threshold, min_cells, log1p flag) inside the summary JSON.
5. Provide guidance on next steps (doublet detection, downstream analysis).

## Guardrails
- Adjust MT% expectations for tissue context; avoid over-filtering rare populations.
- This workflow is QC only—doublet handling and batch correction stay separate.
- Keep reproducibility by storing command invocations and environment info.

## References
- See `README.md`, `qc_core.py`, `qc_analysis.py`, and `qc_plotting.py` for API usage and schema details.