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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Documentation


Publication for Metab

Metab in publications

 (6)
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 […]

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. […]

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 […]

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 […]

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., […]


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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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