Installation

It’s recommended to create a conda environment for running CAME:

conda create -n env_came python=3.8
conda activate env_came

Install required packages:

pip install "scanpy[leiden]"
pip install torch  # >=1.8
pip install dgl

See scanpy (https://scanpy.readthedocs.io/en/stable/), PyTorch (https://pytorch.org/) and DGL(https://www.dgl.ai/) for detailed installation guide (especially for GPU version).

Install CAME

To install CAME with PyPI, run:

pip install came

Or fetch from GitHub and manually install:

git clone https://github.com/zhanglabtools/CAME.git
cd CAME
python setup.py install