SpaCcLink: Exploring downstream signaling regulations with graph attention network for systematic inference of spatial cell-cell communication

Cellular communication is vital for the proper functioning of multicellular organisms. A comprehensive analysis of cellular communication demands the consideration not only of the binding between ligands and receptors but also of a series of downstream signal transduction reactions within cells. Nevertheless, the majority of existing spatial cell-cell communication algorithms fail to take into account the downstream signals within cells. In this study, we put forward SpaCcLink, a cell-cell communication analysis method that takes into account the downstream influence of individual receptors within cells and systematically investigates the spatial patterns of communication as well as downstream signal networks.

User Manual and Tutorial

Before you can use SpaCcLink, you first need to install the necessary libraries, which you can do using the following script

pip install -r requirements.txt

And You can refer to tutorial/melanoma/melanoma.ipynb for the specific usage tutorial.