Is the Single-Cell RNA-seq QC skill free?

Yes. The skill itself is free from biocontext-ai/skill-to-mcp. SkillProof publishes the install command and an independent test verdict at no cost.

What is the Single-Cell RNA-seq QC SkillProof Score?

9.6/10 — installs cleanly 5/5, triggers reliably 5/5, output vs. baseline 9/10, docs & honesty 5/5.

How do I install Single-Cell RNA-seq QC?

Copy the install command from this page, run it in your terminal, and restart Claude Code. Skills live in ~/.claude/skills/ (global) or .claude/skills/ inside a project.

Can I use Single-Cell RNA-seq QC with Cursor, Copilot, Gemini CLI, Codex or other AI tools?

The SKILL.md format is native to Claude (Claude Code, Desktop, claude.ai). The instructions inside adapt to other assistants: Cursor rules, GitHub Copilot instructions, Windsurf rules, Custom GPTs, AGENTS.md for OpenAI Codex, and GEMINI.md for Google Gemini CLI — our conversion guides cover each, and the free converter on the tools page does the wrapping for you.

Single-Cell RNA-seq QC

Automated scverse-style QC for .h5ad/.h5 single-cell data with MAD-based filtering and diagnostic plots.

by biocontext-ai · biocontext-ai/skill-to-mcp

Tested · Works

Install — copy the command Download source ↗

Test report

Verdict: Tested · Works
Score: 9.6/10
Tested: Jul 14, 2026
Environment: Claude Code 2.x (agent harness)
Upstream re-checked: Aug 10, 2026 · 530eecd

Ran scripts/qc_analysis.py end-to-end on a synthetic 300-cell AnnData file: it auto-derived MAD thresholds, flagged 45 outlier cells (15%), and wrote 3 real diagnostic PNGs plus filtered and QC-annotated h5ad outputs -- a fixed-threshold baseline script produced only a filtered file with zero visualizations and no adaptive reasoning.

Scored on four weighted criteria — install, triggering, output vs. baseline, docs. How scoring works

Installs cleanly 5/5
Triggers reliably 5/5
Output vs. baseline 9/10
Docs & honesty 5/5

What Single-Cell RNA-seq QC does

Runs a full single-cell RNA-seq QC pipeline (scripts/qc_analysis.py) or exposes modular functions (qc_core.py, qc_plotting.py) following scverse best practices: MAD-based adaptive outlier detection on counts/genes/mitochondrial%, gene filtering, and before/after diagnostic visualizations. Triggers on QC, filtering, or scverse/scanpy best-practice requests for .h5ad or 10X .h5 files.

How to install Single-Cell RNA-seq QC

git clone https://github.com/biocontext-ai/skill-to-mcp
cd skill-to-mcp
mkdir -p ~/.claude/skills
cp -r skills/single-cell-rna-qc ~/.claude/skills/single-cell-rna-qc

Skills live in ~/.claude/skills/ (global) or .claude/skills/ (per-project). Restart Claude Code after installing.

Commands — how to trigger Single-Cell RNA-seq QC

/single-cell-rna-qc Automated scverse-style QC for .h5ad/.h5 single-cell data with MAD-based filtering and diagnostic plots.

It also activates on plain-language prompts like these:

Run MAD-based QC filtering on my h5ad single-cell dataset
Flag low-count and MT-heavy cells in this AnnData file
Generate diagnostic QC plots for my scRNA-seq data

Frequently asked questions

Is the Single-Cell RNA-seq QC skill free?: Yes. The skill itself is free from biocontext-ai/skill-to-mcp. SkillProof publishes the install command and an independent test verdict at no cost.
Does Single-Cell RNA-seq QC work with Claude Code?: We tested it with Claude Code 2.x (agent harness) on Jul 14, 2026. Verdict: Tested · Works. Ran scripts/qc_analysis.py end-to-end on a synthetic 300-cell AnnData file: it auto-derived MAD thresholds, flagged 45 outlier cells (15%), and wrote 3 real diagnostic PNGs plus filtered and QC-annotated h5ad outputs -- a fixed-threshold baseline script produced only a filtered file with zero visualizations and no adaptive reasoning.
What is the Single-Cell RNA-seq QC SkillProof Score?: 9.6/10 — installs cleanly 5/5, triggers reliably 5/5, output vs. baseline 9/10, docs & honesty 5/5.
How do I install Single-Cell RNA-seq QC?: Copy the install command from this page, run it in your terminal, and restart Claude Code. Skills live in ~/.claude/skills/ (global) or .claude/skills/ inside a project.
Can I use Single-Cell RNA-seq QC with Cursor, Copilot, Gemini CLI, Codex or other AI tools?: The SKILL.md format is native to Claude (Claude Code, Desktop, claude.ai). The instructions inside adapt to other assistants: Cursor rules, GitHub Copilot instructions, Windsurf rules, Custom GPTs, AGENTS.md for OpenAI Codex, and GEMINI.md for Google Gemini CLI — our conversion guides cover each, and the free converter on the tools page does the wrapping for you.