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Installation Guide

Follow the steps below to install and set up CytoBulk.

Setting Up the Environment for Python and R

The CytoBulk package is developed based on the pytorch framework and can be implemented on both GPU and CPU. We recommend running the package on GPU. Please ensure that pytorch and CUDNN are installed correctly.

Option 1: Set Python and R Together

conda config --append channels conda-forge
conda create --name cytobulk python=3.10 r-base=4.4
conda activate cytobulk
pip install cytobulk
This approach is suitable for users who want all dependencies managed within the same Conda environment. However, it might not work reliably on Windows due to potential issues with R configuration in Conda.

If you have installed cytobulk package, please run following code to update the latest version 

pip install cytobulk==0.1.20

Option 2: Set Only Python and Specify R Path Separately

conda create --name cytobulk python=3.10
conda activate cytobulk
pip install cytobulk
Then, before running the main program, you need to specify the path to your locally installed R. This can be done using Python by setting the R_HOME environment variable. Add the following lines at the beginning of your Python script: 
import os
# Set the R installation path (adjust the path based on your R installation)
os.environ['R_HOME'] = r_path
If you have installed cytobulk package, please run following code to update the latest version 
pip install cytobulk==0.1.20

Install required R packages

To run CytoBulk, make sure all the following prerequisites are installed.

R 4.4.0 or higher and the following packages