Installation

Create a virtual environment

We recommend creating a virtual environment using Python 3.11:

conda create -n tiscope python=3.11
conda activate tiscope

Install PyTorch

Install PyTorch following the PyTorch installation guide. For example, on a machine with CUDA 12.x:

pip install torch torchvision --index-url https://download.pytorch.org/whl/cu126

Install PyTorch Geometric

Install PyG following the PyG installation guide. Usually:

pip install torch_geometric

Install dependencies

pip install 'scanpy[leiden]' louvain squidpy ipykernel

Install TISCOPE

Via PyPI:

pip install tiscope

Or from GitHub:

git clone git://github.com/ericli0419/TISCOPE.git
cd TISCOPE
pip install -e .