Installation

PySingleCellNet is available on PyPI. You can install it with:

pip install pySingleCellNet

You could also install it directly from GitHub with:

pip install git+https://github.com/CahanLab/PySingleCellNet.git

From requirements.txt

Clone the repository and install all dependencies:

git clone https://github.com/CahanLab/PySingleCellNet.git
cd PySingleCellNet
pip install -r requirements.txt
pip install -e .

From conda environment.yml

Create and activate a conda environment with all dependencies:

git clone https://github.com/CahanLab/PySingleCellNet.git
cd PySingleCellNet
conda env create -f environment.yml
conda activate pyscn

Jupyter notebooks

To run the tutorial notebooks, install Jupyter in the environment: shell pip install jupyter ipykernel