2.1 Installation

scMINER framework is mainly developed with R for its advantages in statistical analysis and data visualization. It also includes two components, MICA and SJARACNe, that are developed with Python to take its strengths in calculation speed and memory consumption, since mutual information estimation of large-scale scRNA-seq data is usually compute-intensive.

Please install all three components for the full access to scMINER framework.

Install scMINER R package

The scMINER R package requires R 4.2.3 or newer, and can be installed from GitHub with:

# install.packages("devtools")
devtools::install_github("https://github.com/jyyulab/scMINER.git@dev-qpan")

Install MICA and SJARACNe

The recommended method to install MICA and SJARACNe is to use conda dependency manager:

## setup conda env
conda create -n scminer python=3.9.2                # Create a python virtual environment
source activate scminer                             # Activate the virtual environment

## install MICA
git clone https://github.com/jyyulab/MICA           # Clone the MICA repo
cd MICA                                             # Switch to the MICA root directory
pip install .                                       # Install MICA and its dependencies
mica -h                                             # Check if MICA works

## install SJARACNE
cd ..                                               # Switch to conda env folder
git clone https://github.com/jyyulab/SJARACNe.git   # Clone the SJARACNe repo
cd SJARACNe                                         # Switch to the MICA root directory
python setup.py build                               # Build SJARACNe binary
python setup.py install                             # Build SJARACNe binary
sjaracne -h                                         # Check if SJARACNe works