https://github.com/srom/archaea-vs-bacteria

Code from paper "Systematic genome-guided discovery of antagonistic interactions between archaea and bacteria"
https://github.com/srom/archaea-vs-bacteria

antimicrobial archaea bacteria microbiology phylogenetics

Last synced: about 2 months ago
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Code from paper "Systematic genome-guided discovery of antagonistic interactions between archaea and bacteria"

• Host: GitHub
• URL: https://github.com/srom/archaea-vs-bacteria
• Owner: srom
• License: mit
• Created: 2024-08-13T12:31:09.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2024-09-28T15:37:30.000Z (3 months ago)
• Last Synced: 2024-10-14T23:42:17.766Z (2 months ago)
• Topics: antimicrobial, archaea, bacteria, microbiology, phylogenetics
• Language: Jupyter Notebook
• Homepage: https://doi.org/10.1101/2024.09.18.613068
• Size: 43.5 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Archaea vs Bacteria

Code from paper:

>Systematic genome-guided discovery of antagonistic interactions between archaea and bacteria

>

>Romain Strock, Valerie WC Soo, Antoine Hocher, Tobias Warnecke


>bioRxiv 2024.09.18.613068; doi: https://doi.org/10.1101/2024.09.18.613068

## Content

- `notebook/`: python notebooks to reproduce all the figures.

- `src/`: scripts to produce all the data used in the paper. Scripts are referenced in notebooks.

- `figures/`: all unassembled figures as produced by the relevant notebooks.

- `data/`: input data and data produced by the scripts and notebooks in this repo.

## Install

```sh

git clone https://github.com/srom/archaea-vs-bacteria.git

git lfs pull origin main  # optional - see below

cd archaea-vs-bacteria

conda env create -f environment.yml

conda activate AvB

```

Note: some of the larger files in `data/` are tracked with [Git Large File Storage](https://git-lfs.com/). They won't get  downloaded with `git pull` or through GitHub's UI. To download these files, install `git-lfs` and use `git lfs pull`.