geneGATer is a Python package designed to facilitate the identification and ranking of potential communication genes from spatial transcriptomics data. The package integrates an adapted metagene construction method by Hue et al. [2022] and a Graph Attention Network (GAT) to enable the exploration of cell-to-cell communication without relying on explicit cell-type annotations.
The package is the result of the authors master thesis which can be found here. By employing geneGATer, researchers can efficiently recreate the pipeline showcased in the associated thesis. The package also includes visualization tools to aid in the interpretation of the results, providing a comprehensive framework for studying intricate cellular communication networks.
Please refer to the documentation. In particular, the
You need to have Python 3.9 or newer installed on your system. If you don't have Python installed, we recommend installing Mambaforge.
There are several alternative options to install geneGATer:
- Install the latest development version:
pip install git+https://github.com/dertrotl/geneGATer.git@mainSee the changelog.
For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.
Analysis and Methods in Glioblastoma Spatial Transcriptomics, Benjamin Weinert, 2023.