Metabolite-Investigator: an integrated user-friendly workflow for metabolomics multi-study analysis


Motivation Many diseases have a metabolic background, which is increasingly investigated due to improved measurement techniques allowing high-throughput assessment of metabolic features in several body fluids. Integrating data from multiple cohorts is of high importance to obtain robust and reproducible results. However, considerable variability across studies due to differences in sampling, measurement techniques and study populations needs to be accounted for.

Results We present Metabolite-Investigator, a scalable analysis workflow for quantitative metabolomics data from multiple studies. Our tool supports all aspects of data pre-processing including data integration, cleaning, transformation, batch analysis as well as multiple analysis methods including uni- and multivariable factor-metabolite associations, network analysis and factor prioritization in one or more cohorts. Moreover, it allows identifying critical interactions between cohorts and factors affecting metabolite levels and inferring a common covariate model, all via a graphical user interface.

Availability and implementation We constructed Metabolite-Investigator as a free and open web-tool and stand-alone Shiny-app. It is hosted at, the source code is freely available at

Supplementary information Supplementary data are available at Bioinformatics online.

DOI: 10.1093/bioinformatics/btaa967

Projects: Genetical Statistics and Systems Biology

Publication type: Journal article

Journal: Bioinformatics

Editors: Martelli Pier Luigi

Human Diseases: No Human Disease specified

Citation: Bioinformatics,btaa967

Date Published: 16th Nov 2020

Registered Mode: by DOI

Authors: Carl Beuchel, Holger Kirsten, Uta Ceglarek, Markus Scholz

help Submitter
Beuchel, C., Kirsten, H., Ceglarek, U., & Scholz, M. (2020). Metabolite-Investigator: an integrated user-friendly workflow for metabolomics multi-study analysis. In M. Pier Luigi (Ed.), Bioinformatics (Vol. 37, Issue 15, pp. 2218–2220). Oxford University Press (OUP).

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Created: 18th Jan 2021 at 09:35

Last updated: 7th Dec 2021 at 17:58

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