Installation

Software dependencies

scanpy
torch
ttkbootstrap
opencv-python
rpy2
gseapy
PyYAML
...

The use of the mclust algorithm requires the rpy2 package and the mclust package. See https://pypi.org/project/rpy2/ and https://cran.r-project.org/web/packages/mclust/index.html for detail.

Installation

Downloading STABox code from https://github.com/Tidebear/STABox

git clone https://github.com/zhanglabtools/STABox.git
cd STABox

It’s recommended to create a separate conda environment for running STABox

conda create -n env_STABox python=3.8
conda activate env_STABox

Install R environment in python by conda

conda install -c conda-forge r-base

Other required packages are listed in STABox_env.yaml. Please note that we recommend that you install the appropriate version of pytorch and other packages that are not easy to install, depending on the configuration of your computer. (For pytorch installation requirements, see https://pytorch.org/)

Run STABox toolkit

Make sure you run STABox under ‘STABox\src’ path

cd STABox\src
python your_python_file.py