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Scfm

Skill BioTender-max/awesome-bio-agent-skills/skills/pantheon/scfm

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.From its SKILL.md

Install
npx -y skills add BioTender-max/awesome-bio-agent-skills --skill scfm

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

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SKILL.md

1.2 KB, 195 tokens by cl100k_base, as published. Nobody here has run it

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

What ships with it: 2 files

19.6 KB alongside SKILL.md

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