Installation

Prerequisites

The following packages are requirements:

  • r-base=4.1.3

  • python=3.9

  • MATLAB2019b

Enviroments

  • It is recommended to use conda for installation.

# create a virtual environment named DEPF
conda create -n DEPF
# activate the environment
conda activate DEPF

  • python enviroment:

conda install python=3.9
pip install leidenalg

  • R enviroment:

conda install -c conda-forge r-base=4.1.3
conda install -c conda-forge r-devtools
conda install -c conda-forge r-seurat

  • MATLAB enviroment:

Following the official website tutorial: https://ww2.mathworks.cn/downloads/.

  • DEPF dependencies:

# clone DEPF repository
git clone https://github.com/fanyi21/DEPF.git
# # install the dependencies
cd DEPF/DEPF/HierarchicalAutoencoder/
Rscript RequirePackage.R