scBONITA2

Infers Boolean molecular signaling networks using scRNAseq data and prior knowledge networks, performs attractor analysis, and calculates the importance of each node in the network

Setup:

Cloning the scBONITA2 repository

In your terminal, navigate to the directory where you want to install this project and enter

git clone https://github.com/Luminarada80/scBONITA2.git

Navigate to the scBONITA2 directory

cd scBONITA2

Setting up the environment

There are three options for setting up the environment for scBONITA2:

1. Docker: This is the easiest and most reliable method
2. Conda: This requires you to install a version of conda and create an scBonita conda environment. For Mac users with the M1 series chip, use the Docker instructions or download packages individually.
3. Manually install packages: This will take a bit longer, but will get around issues with creating the environment.

Installation guides:

• Docker installation guide
• Conda installation guide
• BlueHive installation guide
• Manual installation guide

Running scBONITA2

Once you have followed one of these guides to set up the environment, try running the tutorial data and read the "How scBONITA2 works" documentation. Each step has a more detailed guide explaining how it all works.