scgpt

Embed and annotate single-cell expression data with the scGPT foundation model.

288|34|Updated Jul 6, 2026

Search Tags:#data analysis #cell type annotation #single-cell data #single-cell biology #gene representation

Ready to run

npx skills add https://github.com/PKU-YuanGroup/OpenAI4S --skill scgpt-pku-yuangroup

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: scgpt
Source: https://github.com/PKU-YuanGroup/OpenAI4S/tree/main/skills/scgpt
Command: npx skills add https://github.com/PKU-YuanGroup/OpenAI4S --skill scgpt-pku-yuangroup

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

scgpt helps users embed and annotate single-cell expression data using a foundation model for single-cell biology, streamlining data analysis and cell type annotation.

Core Features & Use Cases

Embedding Data: Generate embeddings for AnnData for clustering and integration.
Cell Type Annotation: Provides zero-shot or fine-tuned cell-type annotation.
Gene-Level Representation: Offers gene-level representation for perturbation and GRN tasks.
Use Case: If you have AnnData with single-cell RNA sequencing data and want to perform clustering and annotation, scgpt can help automate this process.

Quick Start

Use the scgpt skill to embed data from 'dataset.h5ad' and produce embeddings.

Frequently Asked Questions about scgpt

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I annotate cell types in single-cell RNA sequencing data?▼

To annotate cell types in single-cell RNA sequencing data, you can use the scGPT foundation model to apply zero-shot or fine-tuned cell-type annotation directly to your AnnData objects.

How do I generate embeddings for single-cell expression data?▼

To generate embeddings for single-cell expression data, you process your AnnData files through the scGPT foundation model to produce representations suitable for clustering and data integration.

Does single-cell data annotation with scGPT require a CUDA-capable GPU?▼

Single-cell data annotation with scGPT requires access to a CUDA-capable GPU for processing. This hardware is necessary to run the scGPT foundation model for embedding and annotation tasks.

Can I extract gene-level representations for perturbation analysis from AnnData?▼

You can extract gene-level representations for perturbation and GRN tasks from AnnData using the scGPT foundation model. This provides specific gene representations suited for downstream single-cell biology analysis.

What is the best way to cluster single-cell data using a foundation model?▼

The best way to cluster single-cell data using a foundation model is to generate embeddings from your dataset.h5ad file using scGPT. These embeddings can then be used directly for clustering and integration.