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.
Installs into .claude/skills of the current project.
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---
id: scfm_skills_index
name: Single-Cell Foundation Models Skills Index
description: |
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.
tags: [scfm, foundation-models, scGPT, geneformer, UCE, embeddings]
---
# 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
