Scvi Tools
Othersscvi-toolsScvi Tools is an Agent Skill for general use published in the companion-inc/feynman repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.
Run scvi-tools single-cell workflows. Use when a task asks for scVI/scANVI setup, latent embeddings, batch correction, differential expression, cell annotation, or reproducible AnnData analysis.
QUICK START
How to use this skill
Bring this guide into your coding agent with a prompt tailored to the tool you use.
- Open your project in Codex.
- Copy and paste the prompt below.
- Review files and risks before approving any action.
Prompt to paste
Inspect the Agent Skill at https://github.com/companion-inc/feynman/blob/HEAD/skills/scvi-tools/SKILL.md and all supporting files. Report provenance, permissions, scripts, dependencies, and security risks. Propose an exact installation into .agents/skills/scvi-tools, but wait for my approval before writing files or running scripts.
Copying this prompt does not install or run the skill. Review third-party files before use.
scvi-tools
Use this skill for reproducible scvi-tools analysis.
Workflow:
- Record AnnData path, organism, assay, batch keys, label keys, covariates, train/test split, and filtering choices.
- Verify Python environment, GPU/CPU route, package version, and data availability before training.
- Save preprocessing notebook, model parameters, training logs, latent embeddings, differential-expression tables, and plots.
- Check batch mixing, biological separation, marker consistency, and sensitivity to preprocessing choices.
- Attach exact commands and artifact paths to the final summary.
Keep raw counts, normalized values, and model-derived latent variables clearly separated.