https://github.com/srom/archaea-vs-bacteria
Code from paper "Archaea produce peptidoglycan hydrolases that kill bacteria"
https://github.com/srom/archaea-vs-bacteria
antimicrobial archaea bacteria microbiology phylogenetics
Last synced: 5 months ago
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Code from paper "Archaea produce peptidoglycan hydrolases that kill bacteria"
- Host: GitHub
- URL: https://github.com/srom/archaea-vs-bacteria
- Owner: srom
- License: mit
- Created: 2024-08-13T12:31:09.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2025-05-28T09:55:25.000Z (about 1 year ago)
- Last Synced: 2025-05-28T10:53:23.237Z (about 1 year ago)
- Topics: antimicrobial, archaea, bacteria, microbiology, phylogenetics
- Language: Jupyter Notebook
- Homepage: https://doi.org/10.1101/2024.09.18.613068
- Size: 59.1 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Archaea vs Bacteria
Code from paper:
> Archaea produce peptidoglycan hydrolases that kill bacteria
>
> Romain Strock, Valerie WC Soo, Pauline Misson, Georgia Roumelioti, Pavel V Shliaha, Antoine Hocher, Tobias Warnecke
> PLOS Biology 23(8): e3003235; doi: https://doi.org/10.1371/journal.pbio.3003235
## 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.
- includes supplementary data such as tree alignments or the result of homology search.
## 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`.