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Nucleic Acids Res. 2018 Jul 2;46(W1):W486-W494. doi: 10.1093/nar/gky310.

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis.

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Institute of Parasitology, McGill University, Montreal, Québec, Canada.
Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
Canadian Center for Computational Genomics, McGill University, Montreal, Québec, Canada.
Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.
Department of Human Genetics, McGill University, Montreal, Québec, Canada.
Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada.
Department of Animal Science, McGill University, Montreal, Québec, Canada.


We present a new update to MetaboAnalyst (version 4.0) for comprehensive metabolomic data analysis, interpretation, and integration with other omics data. Since the last major update in 2015, MetaboAnalyst has continued to evolve based on user feedback and technological advancements in the field. For this year's update, four new key features have been added to MetaboAnalyst 4.0, including: (1) real-time R command tracking and display coupled with the release of a companion MetaboAnalystR package; (2) a MS Peaks to Pathways module for prediction of pathway activity from untargeted mass spectral data using the mummichog algorithm; (3) a Biomarker Meta-analysis module for robust biomarker identification through the combination of multiple metabolomic datasets and (4) a Network Explorer module for integrative analysis of metabolomics, metagenomics, and/or transcriptomics data. The user interface of MetaboAnalyst 4.0 has been reengineered to provide a more modern look and feel, as well as to give more space and flexibility to introduce new functions. The underlying knowledgebases (compound libraries, metabolite sets, and metabolic pathways) have also been updated based on the latest data from the Human Metabolome Database (HMDB). A Docker image of MetaboAnalyst is also available to facilitate download and local installation of MetaboAnalyst. MetaboAnalyst 4.0 is freely available at

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