TISCOPE enables integrative and comparative analyses of spatial omics data to reveal condition-associated tissue modules

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Installation

1. We recommend creating a virtual environment using Python 3.11:

conda create -n tiscope python=3.11
conda activate tiscope

2. (Skip if PyTorch is already installed) 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

3. (Skip if PyG is already installed) Install PyG following the PyG installation guide, usually:

pip install torch_geometric

4. Install dependencies:

pip install 'scanpy[leiden]' louvain squidpy ipykernel

5. Install TISCOPE:

Via Pypi:

pip install tiscope

or git clone and install

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

Getting started

Please refer to the Documentation and Tutorial

Release notes

See the changelog.

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