Tissue module discovery in single-cell-resolution spatial transcriptomics data via cell-cell interaction-aware cell embedding

SPACE (SPatial transcriptomics Analysis via Cell Embedding)

Installation

SPACE is implemented in Pytorch framework.
SPACE can be run on CPU devices, and running SPACE on GPU devices if available is recommended.

Software dependencies

Install Pytorch

Please install Pytorch in advance by following the instructions on : https://pytorch.org/get-started/locally/

Install PyTorch Geometric

Please install PyTorch Geometric in advance by following the instructions on : https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html

Install SPACE from PyPI

pip install space-srt

Install SPACE from GitHub

install the latest develop version

git clone https://github.com/zhangqf-lab/SPACE.git
cd SPACE
python setup.py install

Tutorial

A brief tutorial can be found here.（Still in progress）

Citation

If you use SPACE in your research, please cite our paper:

Li, Y., Zhang J., Gao, X., and Zhang, Q.C. Tissue module discovery in single-cell resolution spatial transcriptomics data via cell- cell interaction-aware cell embedding. Cell Systems 2024 (paper)