![]() To use MetaboAnalystR 3.0, first install all package dependencies. In this vignette, we perform end-to-end metabolomics data analysis on the full batch of clinical IBD samples. To demonstrate this new functionality, we provide the "MetaboAnalystR 3.0 Workflow: Towards an Optimized Workflow for Global Metabolomics" vignette, available here as a PDF. In addition, more support for functional interpretation directly from m/z peaks via mummichog2 (PMID: 23861661), and a new pathway-based method to integrate multi'omics data has been added. The version 3.0 aims to improve the current global metabolomics workflow by implementing a fast parameter optimization algorithm for peak picking, and automated identification of the most suitable method for batch effect correction from 12 well-established approaches. After installing and loading the package, users will be able to reproduce the same results from their local computers using the corresponding R command history downloaded from MetaboAnalyst web site, thereby achieving maximum flexibility and reproducibility. The package is synchronized with the MetaboAnalyst web server. MetaboAnalystR 3.0 contains the R functions and libraries underlying the popular MetaboAnalyst web server, including metabolomic data analysis, visualization, and functional interpretation. MetaboAnalystR 3.0: Towards an Optimized Workflow for Global Metabolomics
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