https://github.com/singjc/metagenpipe

https://github.com/singjc/metagenpipe

Last synced: 17 days ago
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• Host: GitHub
• URL: https://github.com/singjc/metagenpipe
• Owner: singjc
• Created: 2021-02-18T16:07:23.000Z (almost 4 years ago)
• Default Branch: master
• Last Pushed: 2023-10-05T03:20:29.000Z (over 1 year ago)
• Last Synced: 2024-05-12T15:50:35.756Z (9 months ago)
• Language: Jupyter Notebook
• Size: 153 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

        
# MetagenPipe

![image](https://github.com/singjc/MetagenPipe/assets/32938975/15c1ca54-95b6-471d-8910-7d8f7b03d038)

Medicine By Design Microbiome Project

## Overview:

Explore and attempt to improve upon classification of healthy and nonhealthy patients based on microbiome species frequencies.

## folders:

* data: where data goes

* data/raw: where raw downloaded data goes

* data/preprocessed: where any data that was produced by our own manipulation goes

* src: where all preprocessing + analysis scripts/notebooks go

## files:

* Dockerfile: makes docker image for this project

* build_image.sh: runs command to build image

* run_docker_it.sh: run an interactive session in Docker container. Note you might have to change some filepaths in this file for it to work on your machine

## Citation

Sing, J. C., Whitley, O., & Davis, S. (2023). Diagnostic Potential of Shallow Depth Gut Metagenomics Sequencing for Atherosclerotic Cardiovascular Disease Risk Stratification. https://doi.org/10.1101/2023.10.02.560614