README.md

# SARS-CoV-2_Manuscript
Code and Data from our SARS-CoV-2 manuscript titled "Immunomodulatory fecal metabolites are associated with mortality in COVID-19 
patients with respiratory failure"

[![DOI](https://zenodo.org/badge/496329437.svg)](https://zenodo.org/badge/latestdoi/496329437)
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R Version (4.1.1)

Performed on MacOS Monterey v 12.2.1

Processor: 2.4 GHz 8-Core Intel Core i9

Memory: 64 GB 2667 MHz DDR4

Graphics: AMD Radeon Pro 5500M 8 GB
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Data Folder
`Data` - Contains all R images (.rds) and a single R Image (.RData) that are used in the analysis


Results Folder
`Results` - Contains all produced figures from the analysis
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To download the data there are two options available. 

Option A) Download the zipped file at: https://zenodo.org/badge/latestdoi/496329437

Option B) Enable Git Large File Storage:

https://git-lfs.github.com/

Then clone the repository:

https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository

Then run the R Markdown. You may need to change the file paths in your R Markdown that you've downloaded (e.g. file paths to the R images)

To download the data: 

Download the zipped file at: https://zenodo.org/badge/latestdoi/496329437