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MetabR specifications

Information


Unique identifier OMICS_06042
Name MetabR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Brynn H. Voy

Publication for MetabR

MetabR citations

 (4)
library_books

From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

2017
GigaScience
PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] iments with limited sample size. Selective Paired Ion Contrast (SPICA) [] is a tool that aims at extracting relevant information from noisy datasets by analyzing ion pairs instead of individual ions. MetabR [] normalizes data using linear mixed models and tests for treatment effects with ANOVA. By contrast, Model Population Analysis–Random Forests (MPA-RF) [] combines random forests with model pop […]

library_books

Metabolic fingerprinting of Arabidopsis thaliana accessions

2015
Front Plant Sci
PMCID: 4444734
PMID: 26074932
DOI: 10.3389/fpls.2015.00365

[…] lite identifications with their compound classes were integrated into a SQLite (https://sqlite.org/) database, which is available as Supplemental Data . For statistical analysis we used the R script “MetabR” (Ernest et al., ), which calculates the fold-changes and p-values according to Tukey's Honest Significant Difference (HSD).The R package and Graphical User Interface (GUI) “Rattle” (Williams, […]

library_books

An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64

2015
PeerJ
PMCID: 4655102
PMID: 26618079
DOI: 10.7717/peerj.1401

[…] lled, as well as MALDIquant/MALDIquantForeign for spectra processing () and MSI.R for evaluating Mass Spectrometry Imaging (MSI) data ().For the linear model analysis of metabolomic data, we included MetabR (http://metabr.r-forge.r-project.org/), which provides a Graphical User Interface (GUI) and can be used for both, statistical data evaluation and data preparation for Mining.Rattle—the R Analyt […]

library_books

Transcriptomic and metabolomic profiling of chicken adipose tissue in response to insulin neutralization and fasting

2012
BMC Genomics
PMCID: 3503602
PMID: 22938590
DOI: 10.1186/1471-2164-13-441

[…] enes [,]. Statistical analysis of metabolomic data was performed using an analysis tool that we developed specifically for metabolomic data analyses (Ernest et al., manuscript in review). The script (metabR), written in the language R, uses linear mixed-effect modeling to normalize metabolomics data containing both fixed- and random-effect confounding variables. The script averages any replicate m […]

Citations

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MetabR institution(s)
Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA

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