# 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.

- Skill: `gabrielmoreira/single-cell-foundation-models-skills-index` (Agent Skill, multi-file: 3 files)
- Install (CLI): `npx skillmds@latest add gabrielmoreira/single-cell-foundation-models-skills-index`
- Raw SKILL.md: https://api.skillmd.com/api/skills/gabrielmoreira/single-cell-foundation-models-skills-index/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: AI & ML
- Author: gabrielmoreira (https://skillmd.com/u/gabrielmoreira)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/gabrielmoreira/single-cell-foundation-models-skills-index

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# 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