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Metab specifications

Information


Unique identifier OMICS_06702
Name Metab
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 1.15.0
Stability Stable
Requirements
BiocGenerics, RUnit, pander, svDialogs, xcms, R(>=3.0.1)
Maintained Yes

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No version available

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Publication for Metab

Metab citations

 (6)
library_books

A comparison of sample preparation methods for extracting volatile organic compounds (VOCs) from equine faeces using HS SPME

2018
Metabolomics
PMCID: 5754382
PMID: 29367839
DOI: 10.1007/s11306-017-1315-7

[…] deconvolution system (amdis-version 2.71, 2012) and the national institute of standards and technology (nist) mass spectral library (version 2.0, 2011) to putatively identify vocs. the r package metab (aggio et al. ) was used to align the data. all samples were analysed in triplicate, an average was taken of the replicates at this stage and taken forward for data analysis to keep random […]

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

[…] mass spectra from gc-ms data and uses it to search mass spectral libraries. a disadvantage of this software is that the output requires extensive treatment to be used for further analysis. however, metab [], an r package based on functions of xcms, was developed to automate the pipeline for analysis of gc-ms data processed by amdis facilitating the use of its results for further data analysis. […]

library_books

Urinary Volatile Organic Compounds for the Detection of Prostate Cancer

2015
PLoS One
PMCID: 4657998
PMID: 26599280
DOI: 10.1371/journal.pone.0143283

[…] the automated mass spectral deconvolution and identification system software (amdis, version 2.71, 2012), the nist mass spectral library (version 2.0, 2011) and the r (r core team, 2013) package metab []. amdis and nist were used to build a voc library containing 197 metabolites present in the urine samples analysed in this study (). a forward and reverse match of 800/1000 and above was used […]

library_books

Identifying and quantifying metabolites by scoring peaks of GC MS data

2014
BMC Bioinformatics
PMCID: 4307155
PMID: 25492550
DOI: 10.1186/s12859-014-0374-2

[…] ion mass fragments from gc-ms files and for the generation of graphical outputs. the reports generated by metabox can be directly applied to other tools, such as metaboanalyst [] and the r package metab [], in order to perform further data processing and statistical analyses. in addition, metabox accepts spectral libraries built using amdis, including the original formats […]

library_books

Methodological approaches to help unravel the intracellular metabolome of Bacillus subtilis

2013
Microb Cell Fact
PMCID: 3722095
PMID: 23844891
DOI: 10.1186/1475-2859-12-69

[…] lc-ms/ms, as well as ce/ms, have been reported. in addition, new convenient tools for data analysis and visualization have been developed, such as mzmine [,] and xcms for ms data []; gavin [] and metab [] for gc-ms analysis; batman [] and bquant [] for nmr analysis as well as, metassimulo [] and mbrole [], metexplore [] and msea [] to handle and visualize data sets of increasing size., […]

library_books

Computational mass spectrometry for small molecules

2013
J Cheminform
PMCID: 3648359
PMID: 23453222
DOI: 10.1186/1758-2946-5-12

[…] identifies metabolites and allows for the analysis of high-throughput data. targetsearch[] iteratively corrects and updates retention time indices for searching and identifying metabolites. metab[] is an r package that automates the pipeline for analysis of metabolomics gc-ms datasets processed by amdis. pyms[] comprises several functions for processing raw gc-ms data, such as noise […]


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Metab institution(s)
Centre for Microbial Innovation, School of Biological Sciences, The University of Auckland, Auckland, New Zealand

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