The part of the tutorial works on linux and macOS and maybe on Windows. You need to install the conda package manager. Download this repo with git or download it as zip archive and extract it.
git clone https://github.com/metagenome-atlas/Tutorial.git
cd Tutorial
The script use various python package for analyzing and plotting. Set them up by running
cd scripts
./setup.sh
This creates a conda-environment in order not to interfere with other software on your computer. Activate the environment by running, then start jupyter:
conda activate analyze
jupyter lab
Click on the Differential_abundance.ipynb and start the differential analysis.