2.10 Metabolomics data sets

Sharing of data has become increasingly common, and metabolomics data are available from MetaboLights [143] in the EU, GNPS [49] and Metabolomics Workbench [144] in the US. In the context of this review, we focus instead on data in R packages, which is important for development, unit testing, documentation and user training (see Table 12). While there is no difference in R between software and data packages per se, they are handled differently in the Bioconductor infrastructure and separate views exist.

There are several data sets with raw data from LC-MS and flow injection analysis, which can be used by the data pre-processing packages in the previous sections. Other packages contain pre-processed data from GC-MS, LC-MS or NMR in the form of peak tables, which are then typically used in statistics packages, network analysis and other downstream analyses.