Single-cell RNA Analysis Skill

An OpenAI4S-maintained workflow for human or mouse, cell-called 10x GEX scRNA-seq and snRNA-seq matrices. It provides a versioned configuration contract, an executable Scanpy pipeline for either single-sample descriptive or donor-aware comparative analysis, conservative scientific gates, restartable checkpoints, and an auditable output bundle. It does not modify or vendor the pinned bioSkills collection.

Install

A Skill is a directory of files, so installing one is copying that directory somewhere an agent looks. With Node 18+ and git on PATH (npm resolves a github: spec through it), and nothing cloned:

npx github:PKU-YuanGroup/OpenAI4S install single-cell-rna-analysis --target claude

--target claude writes to ~/.claude/skills, claude-project to ./.claude/skills, openai4s to <data_dir>/user-skills, and --dir <path> to anywhere you name. The resolved absolute path is printed before anything is written there, and --dry-run stops at that plan. A reinstall refuses to overwrite a copy you have edited or one it did not install, and uninstall removes only the files it wrote. npm 0.2.0 does not include this recipe. Use the GitHub installation command above.

Without Node, take the directory itself — and turn it into a .zip if an upload field wants one. The tarball is the whole repository (over 100 MB), and the pipe is a POSIX shell recipe (macOS, Linux, WSL) that extracts only this directory:

curl -L https://codeload.github.com/PKU-YuanGroup/OpenAI4S/tar.gz/refs/heads/main \
  | tar -xz --strip-components=2 OpenAI4S-main/skills/single-cell-rna-analysis
python3 -m zipfile -c single-cell-rna-analysis.zip single-cell-rna-analysis

The click-through form of that same download is the repository zip, which is also the route to take on Windows: extract it and copy skills/single-cell-rna-analysis/ out (unzip main.zip 'OpenAI4S-main/skills/single-cell-rna-analysis/*' unpacks only that directory). If you already run OpenAI4S there is nothing to install — the wheel ships every bundled Skill, and a bundled Skill takes precedence over a same-named copy in <data_dir>/user-skills. Targets, provenance, and what the installer refuses to do: tools/skills-installer/.

Files

Path	Responsibility
`SKILL.md`	Short agent entry point: scope, public calls, stage routing, failure behavior, Artifact handoff, and interpretation boundaries.
`kernel.py`	Lazy-imported implementation of `preflight(config)`, `run(config, output_dir)`, and `resume(run_dir)`.
`references/`	Detailed input, scientific, annotation, statistical, and output contracts, with its own bilingual directory documentation.

The workflow is evidence preserving: raw counts remain isolated in layers["counts"], Harmony changes an embedding only, cluster markers never stand in for condition DE, and unconfirmed labels may remain Unknown.