scgpt

scgpt is a skill for Claude Code, Codex from HughYau/AcademicForge. It costs 89 tokens per session (1,368 once invoked), scanned A, original, no licence file.

A guide for using scGPT, an AI model trained on single-cell biology data, with single-cell gene-expression data. It works with AnnData, a common format for storing this kind of data.

In plain words
What is it for?
Use it to create cell representations for clustering or combining datasets, identify cell types without additional training, and study genes in perturbation or gene-regulation tasks.
Why use it?
It helps researchers represent, group, and label individual cells without building those workflows from scratch.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit Use it to create cell representations for clustering or combining datasets, identify cell types without additional training, and study genes in perturbation or gene-regulation tasks.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/hughyau/academicforge/scgpt
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 HughYau/AcademicForge --skill scgpt
Clone the repo
git clone --depth 1 https://github.com/HughYau/AcademicForge

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.

agentmods badge for scgpt

README.md
[![agentmods](https://agentmods.dev/badge/skills/hughyau/academicforge/scgpt.svg)](https://agentmods.dev/skills/hughyau/academicforge/scgpt)
Your own site
<a href="https://agentmods.dev/skills/hughyau/academicforge/scgpt"><img src="https://agentmods.dev/badge/skills/hughyau/academicforge/scgpt.svg" alt="Measured on agentmods" height="20"></a>
Per session 89 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,368 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 unknown 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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00089 $0.01368
Opus 5 $0.00044 $0.00684
Sonnet 5 $0.00018 $0.00274
Haiku 4.5 $0.00009 $0.00137

Measured 8d ago against content hash 7af27c91d22a, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-07, from the pricing page.

Security

Grade A, and why

scgpt 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 8d 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.

skills/claude-science/scgpt/SKILL.md · 150 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

Files

What ships with it

1 file 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.

  1. 8d ago First seen · 150 lines · 89 tokens per session scan A 7af27c91d22a

Subscribe to this mod's changes

scgpt is a skill published in the GitHub repository HughYau/AcademicForge (2,521 stars, last pushed 8d ago), with no licence file. It adds 89 tokens to every session and 1,368 once invoked, about $0.0004 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.

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