scArches requires Python 3.7 or 3.8. We recommend to use Miniconda.


The easiest way to get scArches is through pip using the following command:

sudo pip install -U scarches

Conda Environment

You can also use our environment file. This will create the conda environment ‘scarches’ with the required dependencies:

git clone
cd scarches
conda env create -f envs/scarches_linux.yaml
conda activate scarches


You can also get the latest development version of scArches from Github using the following steps: First, clone scArches using git:

git clone

Then, cd to the scArches folder and run the install command:

cd scarches
python3 install

On Windows machines you may need to download a C++ compiler if you wish to build from source yourself.


The list of dependencies for scArches can be found in the requirements.txt file in the repository.

If you run into issues, do not hesitate to approach us or raise a GitHub issue.