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MetabolAnalyze specifications


Unique identifier OMICS_30354
Name MetabolAnalyze
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.3
Stability Stable
gplots, gtools, ellipse, mvtnorm, mclust
Source code URL
Maintained Yes


No version available



  • person_outline Claire Gormley

Publication for MetabolAnalyze

MetabolAnalyze citations


Promising Prebiotic Candidate Established by Evaluation of Lactitol, Lactulose, Raffinose, and Oligofructose for Maintenance of a Lactobacillus Dominated Vaginal Microbiota

Appl Environ Microbiol
PMCID: 5812932
PMID: 29269494
DOI: 10.1128/AEM.02200-17

[…] log base 2 transformation. The log-transformed mass list was then exported as a single txt file and used for all further analyses. For principal-component analysis, data were Pareto scaled using the MetabolAnalyze package in R. Principal components were then plotted using the pca function from the FactoMineR package in R. Identities of metabolites were determined by authentic standards based on a […]


Improving Metabolic Health Through Precision Dietetics in Mice

PMCID: 5753872
PMID: 29158425
DOI: 10.1534/genetics.117.300536

[…] es were identified using the Human Metabolome Database (). Once metabolites were adjusted for tissue weight and internal standard, each metabolite was pareto-scaled across all mice using the package “MetabolAnalyze” (). Each mouse was median normalized across all metabolites and metabolites transformed using cube root. The model assessed in each strain was:Metabolite=diet+sex.Statistical analyses […]


Novel application of heuristic optimisation enables the creation and thorough evaluation of robust support vector machine ensembles for machine learning applications

PMCID: 4655007
PMID: 26617479
DOI: 10.1007/s11306-015-0894-4

[…] To demonstrate the use of the classyfire package, it was applied to two well-understood NMR datasets, both of which are included in the publicly available MetabolAnalyze R package ( These are simulated datasets designed to mimic experimental data previously reported in Carmody and Brennan (), and Nyamund […]


Delving deeper into technological innovations to understand differences in rice quality

PMCID: 4883128
PMID: 26054242
DOI: 10.1186/s12284-015-0043-8

[…] all data (van den Berg et al. ): for each variable, data was centred on a mean of zero and the variance scaled by dividing by the square root of the standard deviation for each variable (R package: ‘MetabolAnalyze’, (Gift et al. )). We used Principal Components Analysis (PCA) (R package: ‘FactoMineR’, (Husson et al. )) to extract the first two dimensions in our data that explained the greatest am […]

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MetabolAnalyze institution(s)
School of Mathematical Sciences, University College Dublin, Ireland; School of Agriculture, Food Science and Veterinary Medicine, Conway Institute, University College Dublin, Ireland
MetabolAnalyze funding source(s)
Supported by the Irish Research Council for Science Engineering and Technology (IRCSET) funded PhD Programme in Bioinformatics and Systems Biology in University College Dublin, Ireland.

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