A repository containing everything participants of the post-graduate course will need to complete the workshop concerning metabolomics data processing.
This course will give a basic introduction on (untargeted) preprocessing of liquid chromatography coupled to mass spectrometry (LC-MS) (also extendable to GC-MS or LC-MS/MS) based metabolomics. The methods and workflow presented in this course our mainly based on the workflow presented by the xcms package on Bioconductor.
For this course, you will need R version > 4.4.
You can download and install R here
And Rstudio can be downloaded and installed from here
The packages needed to complete the course can be installed by running the next code block:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("xcms")
install.packages("remotes")
remotes::install_github("https://github.com/wkumler/squallms")
install.packages("RColorBrewer")
install.packages("RaMS")
install.packages("ggplot2")
install.packages("dplyr")
Download the Github repository as a .zip file and extract in a working directory to your liking. Then open the .RProj file to start the workshop.
