gabrielmoreira 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