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https://github.com/ku-cbd/PhageBoost
Rapid discovery of novel prophages using biological feature engineering and machine learning
https://github.com/ku-cbd/PhageBoost
Last synced: about 1 month ago
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Rapid discovery of novel prophages using biological feature engineering and machine learning
- Host: GitHub
- URL: https://github.com/ku-cbd/PhageBoost
- Owner: ku-cbd
- License: gpl-3.0
- Created: 2020-06-26T17:51:40.000Z (about 4 years ago)
- Default Branch: master
- Last Pushed: 2022-09-12T13:19:37.000Z (almost 2 years ago)
- Last Synced: 2024-05-16T13:02:38.545Z (about 1 month ago)
- Language: Jupyter Notebook
- Size: 36.2 MB
- Stars: 32
- Watchers: 5
- Forks: 5
- Open Issues: 23
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Lists
- awesome-phages - PhageBoost - Rapid discovery of novel prophages using biological feature (Annotation / Prophage prediction)
README
# PhageBoost
Rapid discovery of novel prophages using biological feature engineering and machine learning
TBA
## Introduction
Prophage predictor based on gene features against a background.
Prophages are phages integrated into prokaryotic genomes that drive many aspects of bacterial biology. Their extreme diversity means they are challenging to detect using sequence similarity. We present a novel fast and generalizing machine learning method to facilitate novel phage discovery.
## Publications
Sirén,K., Millard,A., Petersen,B., Gilbert,M.T.P., Clokie,M.R.J. and Sicheritz-Pontén,T. (2020) Rapid discovery of novel prophages using biological feature engineering and machine learning. 10.1101/2020.08.09.243022.
https://www.biorxiv.org/content/10.1101/2020.08.09.243022v1.abstract
## Getting Started
### Installation
###
For now PhageBoost needs XGBoost 1.02
#### from PyPI
```
conda create -y -n PhageBoost-env python=3.7
conda activate PhageBoost-env
pip install PhageBoost
PhageBoost -h
```
#### from GitHub
```
conda create -y -n PhageBoost-env python=3.7
conda activate PhageBoost-env
git clone [email protected]:ku-cbd/PhageBoost.git
cd PhageBoost/
python setup.py bdist_wheel
pip install --user .
PhageBoost -h
```
### CLI
```
PhageBoost -h
PhageBoost -f example/data/NC_000907.fasta.gz -o results
```
### Notebooks
There are basic notebook examples in the ```notebooks/```
These notebooks provide a way how to bring your own genecalls to PhageBoost.
You can connect your PhageBoost kernel to your pre-existing Jupyter via ipykernel:
```
conda activate PhageBoost
pip install ipykernel
python -m ipykernel install --user --name PhageBoost --display-name "PhageBoost"
```