MWASTools is an R package designed to provide an integrated pipeline to analyse metabonomic data in large-scale epidemiological studies. Key functionalities of our package include: quality control analysis; metabolome-wide association analysis using various models (partial correlations, generalized linear models); visualization of statistical outcomes; metabolite assignment using statistical total correlation spectroscopy (STOCSY); and biological interpretation of metabolome-wide association studies results.

Availability and implementation

The MWASTools R package is implemented in R (version  > =3.4) and is available from Bioconductor:

Supplementary data are available at Bioinformatics online.

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