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.