The repository contains code to reproduce analyses included in our publication: Deep embeddings to comprehend and visualize microbiome protein space
To download data (embeddings) used in the notebooks run:
./download-data.sh
Data will be downloaded to data
folder.
- [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html)
- timelimit (sudo apt install timelimit)
conda env create --file environment.yml
conda activate mpe
Now environment is ready to run the notebooks.
If you find the repository useful, please cite our paper.
@article{odrzywolek2022,
title={Deep embeddings to comprehend and visualize microbiome protein space},
author={Odrzywolek, Krzysztof and Karwowska, Zuzanna and Majta, Jan and Byrski, Aleksander and Milanowska-Zabel, Kaja and Kosciolek, Tomasz},
journal={Scientific reports},
volume={12},
number={1},
pages={1--15},
year={2022},
publisher={Nature Publishing Group}
}