Single-Cell Foundation Models Skills Index
Workflow guidance and model reference for single-cell foundation models (scGPT, Geneformer, UCE, scBERT, etc.). Covers model selection, validation-first workflow, and per-model I/O contracts.
npx skills add BioTender-max/awesome-bio-agent-skills --skill scfm --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Single-Cell Foundation Models (SCFM) Workflow and model reference for embedding and integration with single-cell foundation models. ## Available Skills ### SCFM Workflow Validation-first workflow for foundation model usage: profile, validate, run, interpret. **Skill file**: [workflow.md](./workflow.md) ### SCFM Model Reference Per-model reference cards with I/O contracts, gene ID schemes, and hardware requirements. **Skill file**: [models.md](./models.md) ### Detailed Model Documentation In-depth specs for individual models (scBERT, scGPT, Geneformer, UCE, etc.). **Docs folder**: [_docs/](./_docs/) ## When to Use - You want FM embeddings (e.g., `obsm["X_uce"]`, `obsm["X_scGPT"]`) - You need model selection based on gene ID scheme and species - You want a validation-first workflow before heavy inference
- Available Skills
- SCFM Workflow
- SCFM Model Reference
- Detailed Model Documentation
- When to Use
What does the Single-Cell Foundation Models Skills Index skill do?
Workflow guidance and model reference for single-cell foundation models (scGPT, Geneformer, UCE, scBERT, etc.). Covers model selection, validation-first workflow, and per-model I/O contracts.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill scfm --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.