space-srt 0.7.0

SPatial transcriptomics Analysis via Cell Embedding

Spatial transcriptomics data analysis via interaction-aware cell embedding reveals cell communities with characteristic cell-cell interactions

SPACE (SPatial transcriptomics Analysis via Cell Embedding)

Installation

install from PyPI

pip install space-srt

install from GitHub

install the latest develop version

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

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

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 (Accepted)