bowang-lab/scGPT

Health v2 · maintenance only

Adoption not part of the score

1620 stars · 341 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

scGPT is a foundation model for single-cell multi-omics built with a generative transformer, providing pretrained checkpoints and a Python package for analysis tasks like cell embedding, integration, and reference mapping. It is the official codebase from Bowang Lab with tutorials, documentation, and PyPI distribution.

Use cases

• analyze single-cell RNA-seq data with a pretrained foundation model
• generate cell embeddings for scRNA-seq datasets
• map query cells to a large reference atlas like CellXGene
• integrate single-cell datasets across batches
• pretrain a transformer model on single-cell multi-omics data
• run zero-shot cell type annotation

When to choose

• you need state-of-the-art pretrained models for single-cell analysis
• you want reference mapping against millions of cells efficiently
• you work in Python with PyTorch and want notebook tutorials

When to avoid

• you need bulk RNA-seq or non-single-cell genomics tools
• you lack GPU resources for large model inference or training
• you need a production web service rather than a research library

Facets

library · maturity active

machine-learning deep-learning llm-training bioinformatics machine-learning artificial-intelligence python single-cell foundation-model transformer genomics multi-omics generative-ai gpu

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markdown · JSON · MCP: product_card(name="bowang-lab/scGPT")