What is Single-Cell Foundation Models Skills Index?

A reference and workflow for single-cell foundation models, which are machine-learning models trained on gene-expression data from individual cells. It covers models such as scGPT, Geneformer, UCE, and scBERT.

Selecting a model, validating input data, creating cell embeddings, combining datasets, and interpreting results from single-cell foundation models.

Choosing and running these models can be difficult because they expect particular gene identifiers, species, data formats, and hardware. The workflow checks those requirements before expensive analysis.

Single-Cell Foundation Models Skills Index — Skill for Claude Code and

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add aristoteleo/PantheonOS --skill scfm

Clone the repo

git clone --depth 1 https://github.com/aristoteleo/PantheonOS

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/aristoteleo/pantheonos/scfm/github.svg)](https://agentmods.dev/skills/aristoteleo/pantheonos/scfm)

Your own site

<a href="https://agentmods.dev/skills/aristoteleo/pantheonos/scfm"><img src="https://agentmods.dev/badge/skills/aristoteleo/pantheonos/scfm/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/aristoteleo/pantheonos/scfm"><img src="https://agentmods.dev/badge/skills/aristoteleo/pantheonos/scfm.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 49 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 285 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits

NVIDIA SkillSpector pass 7 Sept 2026

How audits are shown

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00049	$0.00285
Opus 5	$0.00024	$0.00143
Sonnet 5	$0.00010	$0.00057
Haiku 4.5	$0.00005	$0.00028

Measured 10d ago against content hash 76c4eee1d97d, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

Single-Cell Foundation Models Skills Index scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 10d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

pantheon/factory/templates/skills/omics/scfm/SKILL.md · 41 lines

What it actually says

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

Files

What ships with it

23 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

10d ago First seen · 41 lines · 49 tokens per session scan A 76c4eee1d97d

Subscribe to this mod's changes

Single-Cell Foundation Models Skills Index is a skill published in the GitHub repository aristoteleo/PantheonOS (484 stars, last pushed yesterday), licensed BSD-2-Clause. It adds 49 tokens to every session and 285 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Data and AI Scientific UCE agent ai ai-agents embeddings foundation-models geneformer pantheonos scGPT scfm singlecell spatial-transcriptomics

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