Welcome to Metabonaut! 🧑🚀
This initiative presents a series of workflows based on a small LC-MS/MS dataset, utilizing R and Bioconductor packages. Throughout these workflows, we demonstrate how to adapt various algorithms to specific datasets and how to seamlessly integrate R packages to ensure efficient, reproducible processing.
The primary workflow is the "Complete End-to-End LC-MS/MS Metabolomic Data Analysis".
The full R code for all examples, along with detailed descriptions, is available in the end-to-end-untargeted-metabolomics.qmd file. This file can be opened in RStudio, allowing you to execute each individual R command.
Other vignettes on this website are interlinked, and you can find a detailed description of the dataset used throughout here.
We strive for reproducibility. These workflows are designed to remain stable over time, allowing you to run all the vignettes together as one comprehensive "super-vignette". Any major change will be document here and for smaller updates check the News
The tutorials provided assume that users have basic knowledge of R and RMarkdown. If you're unfamiliar with either, we recommend completing a short tutorial to help you test the code and adapt it to your data. The vignettes are written in Quarto format, to learn more about this go here, this is a farily new format, and some functionallity are shared with the RMarkdown format, therefore learning about it can be usefull to you too.
For basic R course and documentation, I would recommand to check out this website or try an interactive course here for a fun introduction to basic R programming. This cheatsheet could also be of help.
This is just the beginning of our Metabonaut journey, and the website is still being refined. We're actively addressing any ongoing issues. If we're aware of a problem, we'll list it below.
Currently, there are no known issues with the code. If you encounter any, please ensure you have the latest versions of all required packages (as detailed above). If the issue persists, please report it with a reproducible example on GitHub here.
If you encounter any other issues, don't hesitate to let us know!
For contributions, please see the RforMassSpectrometry contributions guideline.
Please review the RforMassSpectrometry Code of Conduct.