Installation

scSpecies requires Python 3.11 or higher.

Virtual environment

It’s best to install scSpecies in an isolated environment:

# Using Python’s built-in venv
python3 -m venv scspecies-env
source scspecies-env/bin/activate

# Using conda
conda create -n scspecies-env python=3.11
conda activate scspecies-env

Install from PyPI

To install the latest stable release of scSpecies run the following command.

pip install scspecies

After installation, confirm that scSpecies loads:

python -c "import scspecies; print(scspecies.__version__)"

Tutorial notebooks

Start with running the tutorial notebooks. They can be downloaded from the GitHub repository.