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Phenotype Associated Spatial Signature Analysis with Graph-based Embedding

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# PASSAGE
Learning phenotype associated signature in spatial transcriptomics with PASSAGE
![Model architecture](https://raw.githubusercontent.com/gao-lab/PASSAGE/main/model.png)

## Environment
```
mamba env create -f passage_environment.yaml
mamba activate passage
```

## Installation
```
git clone https://github.com/gao-lab/PASSAGE
cd PASSAGE
python setup.py build
python setup.py install
```
## Tutorial
For usage, please see the jupyter-notebook example [here](./tutorial/tutorial.ipynb). The data used in the tutorial is available in the jupyter-notebook and the following figshare link: https://figshare.com/articles/dataset/tutorial_data_of_PASSAGE_model/28539134.

## Citations
Guo, C. K., Xia, C. R., Peng, G., Cao, Z. J., & Gao, G. (2024). Learning phenotype associated signature in spatial transcriptomics with PASSAGE. Small Methods, 2401451. (https://onlinelibrary.wiley.com/doi/abs/10.1002/smtd.202401451)

PASSAGE

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