Installation

scBIOT follows the lightweight installation pattern: install the stable PyPI release or use an editable checkout for development and notebooks.

Install from PyPI

The published wheels include all core dependencies:

pip install scbiot

Editable install

Clone the repository if you want to run the example notebooks or contribute:

git clone https://github.com/haihuilab/scbiot.git
cd scbiot
pip install -e .

Test your setup

Confirm that the package imports and report the installed version:

import scbiot
print(scbiot.__version__)

If you see an ImportError after installation, upgrade pip/setuptools and retry the command. GPU users should install a CUDA-matching build of torch, faiss-gpu or jax[cuda12] before installing scBIOT to ensure the correct binaries are picked up.