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Microbiome Protein Embeddings

The repository contains code to reproduce analyses included in our publication: Deep embeddings to comprehend and visualize microbiome protein space

Download data

To download data (embeddings) used in the notebooks run:

./download-data.sh

Data will be downloaded to data folder.

How to set up environment

Install required tools

- [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html)
- timelimit (sudo apt install timelimit)

Create environment and install dependencies

conda env create --file environment.yml

Activate the environment

conda activate mpe

Now environment is ready to run the notebooks.

Citation Guidelines

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}
}

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Code for the ArdiMiPE publication

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