scgpt
Use scGPT-style single-cell foundation model workflows. Use when a task asks for single-cell embeddings, perturbation prediction, cell annotation, batch transfer, or gene-program analysis.
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scGPT
Use this skill for single-cell foundation model analysis.
Workflow:
- Record dataset source, organism, modality, preprocessing, gene identifiers, cell labels, and perturbation design.
- Verify model/checkpoint/package availability before running.
- Save AnnData or matrix manifests, preprocessing code, model version, embeddings, predictions, plots, and logs.
- Compare labels or predictions against source metadata, marker genes, perturbation controls, and literature.
- Preserve batch, donor, disease, and assay provenance in every summary table.
Do not present cell-state labels without marker or metadata support.
- Repository
- companion-inc/feynman
- Commit
95c51d9
- Last updated
- First committed
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