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

SCFM Model Reference

Per-model reference cards with I/O contracts, gene ID schemes, and hardware requirements.

Skill file: models.md

Detailed Model Documentation

In-depth specs for individual models (scBERT, scGPT, Geneformer, UCE, etc.).

Docs folder: _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