Preface

The term metaRbolomics has been coined for a workshop at the 2016 annual conference of the international Metabolomics society in Dublin, Ireland. On May 11, 2016, a small team of authors started to compile a review of “a few R packages” and how they can be used to do metabolomics data analysis. After some hiatus, Jan Stanstrup revived the idea and this turned into a 60+ page review (accepted in MDPI Metabolites) with more than 200 packages and more than 300 references. But the journey did not end there. In march 2018 Egon Willighagen suggested that this effort should turn into a book, and more importantly, should become a community effort, with more introduction and also include code examples. It now found a home at RforMassSpectrometry, a community website dedicated to R software for the analysis and interpretation of high throughput mass spectrometry assays, including proteomics and metabolomics experiments.

How to …

… download data
The list of packages found in the tables in this book can be downloaded from public/data/AllMetaRbolomicsTables.csv.

… add packages to the tables
Go to the googlesheet and add the package. Please be careful with adding it to the right section. If it belongs in more than one table add it mulitple times as appropiate.

The package will not appear instantly in the book but only after a change is made to the book itself. You can also open an issue and request the reload such that the package shows up.

… contribute to the text
There are several options. In order of convenience for the maintainer you can:

  • make a pull request on the GitHub repository. You will find the text in the rmd folder.
  • open an issue with the text you want to contribute. Clearly indicate where the text belongs.
  • Send your contribution by email to jst( a t )nexs.ku.dk.

Remember to add yourself to author contributions.

This book in other formats

The book is also available as static PDF file, and as ePUB.