Welcome to scGPT’s documentation!

Welcome to the documentation for scGPT, a Python package for single-cell multi-omic data analysis using pretrained foundation models. This package is based on the work of scGPT (GitHub, preprint) and provides a set of functions for data preprocessing, visualization, and model evaluation.

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Getting Started:

• Introduction
• installation

Tutorials:

• GRN Inference on Pre-trained Model
• Fine-tuning on Pre-trained Model with Batch Integration
• Fine-tuning on Pre-trained Model for Cell-type Annotation
• Fine-tuning Pre-trained Model for Perturbation Prediction
• Reference Mapping Using cell embedding by pretrained scGPT model

API Reference:

• scgpt package
  • Modules
  • scgpt.data_collator
  • scgpt.data_sampler
  • scgpt.loss
  • scgpt.preprocess
  • scgpt.trainer

References:

• FAQ
• References

Indices and tables

• Index

• Module Index

• Search Page