Installation

System Requirements

Hardware requirements

scAGDE package requires only a standard computer with enough RAM to support the in-memory operations.

Software requirements

OS Requirements

This package is supported for Linux. The package has been tested on the following systems:

Linux: Ubuntu 18.04

Python Dependencies

scAGDE mainly depends on the Python scientific stack.

numpy
scipy
torch
scikit-learn
pandas
scanpy
anndata
rpy2

For specific setting, please see requirements.text.

R Dependencies

We need your environment to have R and mclust package installed.

Installation Guide:

You can create an environment to run scAGDE without any problems by following the code below:

conda create -n scagde python=3.9.13 -y
conda activate scagde
pip install torch==2.0.1
pip install numpy==1.26.4
pip install rpy2==3.5.16
pip install scanpy==1.9.3
pip install matplotlib==3.5.0
pip install leidenalg==0.10.2
conda install r-base==4.3.1 -y
conda install r-mclust -y
pip install scAGDE