Installation

CloneOT requires Python 3.10 or later and PyTorch. We recommend installing PyTorch with the right compute platform (CUDA or CPU) from the PyTorch website first. CloneOT runs on a CPU, but a GPU makes training much faster.

Install CloneOT from GitHub:

pip install git+https://github.com/poseidonchan/CloneOT.git

or from a local clone, together with the test and documentation tools:

git clone https://github.com/poseidonchan/CloneOT.git
cd CloneOT
pip install -e ".[test,docs]"
pytest

The dependencies are NumPy, SciPy, pandas, PyTorch, AnnData, Scanpy, scikit-misc (for Seurat v3 gene selection), scikit-learn, Matplotlib and tqdm. The scripts that reproduce the paper need a few more packages, which are installed with pip install -e ".[experiments]".