Installation

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

PyPI

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 https://github.com/theislab/scarches
cd scarches
conda env create -f envs/scarches_linux.yml
conda activate scarches

Development

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

git clone https://github.com/theislab/scarches

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

cd scarches
python3 setup.py install

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

Dependencies

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.