scGPT
SkillProductivityRuns scGPT-style single-cell analysis like cell annotation, embeddings, and perturbation prediction on gene datasets.
Available today. Use it from your connected AI after setup.
No other account needed.
Connect ahel once, and every AI you use reads what you have installed.
Then ask your AI: use the scGPT skill
About this capability
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.
What this skill tells your AI
The instructions your AI receives, as published by companion-inc/feynman in skills/scgpt/SKILL.md and read by ahel’s review.
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.
Signals
- GitHub stars
- 9k
- Forks
- 1k
- Last commit
- Sep 2026
Advanced
- Catalog kind
- skill
- Gateway key
scgpt- Source
- github.com/companion-inc/feynman