GVHD virome analyses

This repository contains the R package gvhdvirome, which contains the data and code for reproducible virome analyses in the paper "..." by ...

Installation

You can install the development version of gvhdvirome with:

# install.packages(c()"devtools", "renv"))
devtools::install_github("rujinlong/gvhdvirome")
renv::restore()

Raw data are not included in the package. To download the raw data, run the following code:

wget https://www.dropbox.com/xxxxxx/gvhdvirome_data.tar.gz   # TODO: update link
tar -xvzf gvhdvirome_data.tar.gz
mkdir -p ${PRJDIR}/workflow/data/00-raw
mv gvhdvirome_data ${PRJDIR}/workflow/data/00-raw

Reproducible analyses

The analyses in the paper can be reproduced by running code in the workflow directory. Each file in the workflow directory is a Quarto document that contains the code and results for a specific analysis. The code in each file can be run in RStudio by clicking the "Run Document" button in the top right corner of the editor pane. The results of each analysis are saved in the data/<analysis_name> directory, where <analysis_name> is the file name of the analysis.