This is the code to go with the XCMS book chapter 2019
There are two workflows in XCMS, the original workflow and the updated workflow. Both of the workflows have their own R notebooks with code explainations of each section.
To First clone the repository :
git clone https://github.com/hpbenton/xcms_book_chapter.git xcmsBook
cd xcmsBook
Data is contained inside zip files. Each file has been independantly zipped up. On linux based system users can run the following code after cloneing the repository.
find . -name "*.zip" | xargs -P 5 -I fileName sh -c 'unzip -o -d "$(dirname "fileName")/$(basename -s .zip "fileName")" "fileName"'
You can then run the R notebook in RStudio by clicking on the Rproj file.
Scripps Research Institute
H. Paul Benton