Installation

Dependency

numpy==1.24.4
pandas==2.0.3
scipy==1.9.3
scikit-learn==1.3.2
louvain==0.8.0,
leidenalg==0.9.1,
anndata==0.9.2
networkx==3.1
scanpy==1.9.8
episcanpy==0.3.2
genomicranges==0.4.2
iranges==0.2.1
biocutils==0.1.3
torch==2.0.0
torch-geometric==2.3.1

These dependencies will be automatically installed along with PRESENT.

Installation via PyPI

PRESENT is available on PyPI here and can be installed via:

pip install bio-present
pip install pyg_lib==0.2.0 torch_sparse==0.6.17 torch_cluster==1.6.1 torch_scatter==2.1.1 -f https://data.pyg.org/whl/torch-2.0.0+cu118.html

Installation via GitHub

PRESENT can also installed from GitHub via:

git clone https://github.com/lizhen18THU/PRESENT.git
cd PRESENT
python setup.py install
pip install pyg_lib==0.2.0 torch_sparse==0.6.17 torch_cluster==1.6.1 torch_scatter==2.1.1 -f https://data.pyg.org/whl/torch-2.0.0+cu118.html