Installation

A functioning python environment (>=3.8) is necessary to run this package.

This package uses the tensorflow (>= 2.4) and tensorflow-probability (>=0.12) packages. The GPU versions of these packages have not been tested with scCODA and are thus not recommended.

To install scCODA via pip, call:

pip install sccoda

To install scCODA from source:

  • Navigate to the directory you want scCODA in

  • Clone the repository from github:

    git clone https://github.com/theislab/scCODA
    
  • Navigate to the root directory of scCODA:

    cd scCODA
    
  • Install dependencies:

    pip install -r requirements.txt
    

Import scCODA in a Python session via:

import sccoda