MVAPACK protocols

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MVAPACK specifications

Information


Unique identifier OMICS_03368
Name MVAPACK
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline MVAPACK <>

Publication for MVAPACK

MVAPACK in pipelines

 (2)
2018
PMCID: 5809546
PMID: 29479299
DOI: 10.1007/s11306-018-1321-4

[…] packages for nmr statistical spectroscopy have been developed including, metassimulo (muncey et al. ), automics (wang et al. ), statistical total correlation spectroscopy (cloarec et al. , ), and mvapack (worley and powers )., for relatively simple biofluids such as serum, plasma, cerebrospinal fluid (csf), fecal water, juice, wine or beer, nmr spectral deconvolution approaches appear to work […]

2014
PMCID: 4165433
PMID: 25228990
DOI: 10.1186/2049-3002-2-18

[…] to generate plots of principal component analysis (pca) and orthogonal projections to latent structures discriminant analysis (opls-da) scores and backscaled loadings (additional file ) using our mvapack software []. metabolite identification from the 1d 1h nmr spectra was accomplished using the chenomx nmr suite 7.6 (http://www.chenomx.com/) and the backscaled loadings., the 2d 1h-13c […]


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MVAPACK in publications

 (7)
PMCID: 5879681
PMID: 29507209
DOI: 10.1073/pnas.1718304115

[…] 15n) txi probe (bruker biospin) at 4 °c as described in the histology, sample quality assessment, and comparison of pet and gamma-counter uptake section below., the nmr data were analyzed using the mvapack () package in gnu octave (). the fid files were apodized, phase corrected, and fourier transformed under the default settings. for comparison, the real parts of the fourier transformed […]

PMCID: 5821832
PMID: 29467421
DOI: 10.1038/s41598-018-20121-w

[…] such databases and tools, for example, include the human metabolome database, biological magnetic resonance data bank, 1h (13c) toccata,, spinassign, spincouple, metaboanalyst, nmrshiftdb, mvapack, rnmr, batman, statistical total correlation spectroscopy, fragment-assembly approach, and signal enhancement by spectral integration (sensi) method., in the fields of nmr-based metabolomics, […]

PMCID: 5809546
PMID: 29479299
DOI: 10.1007/s11306-018-1321-4

[…] that are widely used and which we highly recommend. these include: metaboanalyst (xia et al. , ; xia and wishart ) for multivariate analysis, metabolite annotation and biological interpretation, mvapack for multivariate analysis (worley and powers ), workflow4metabolomics for multivariate analysis (giacomoni et al. ), metassimulo for multivariate analysis (muncey et al. ), the human […]

PMCID: 5487993
PMID: 28538683
DOI: 10.3390/metabo7020022

[…] l/h. we preprocessed the acquired mass spectra with background subtraction, followed by uniform binning with a 0.5 m/z bin size and spectral noise region removal. nmr spectra were processed with our mvapack [] software and automatically phased and normalized using our phase-scatter correction (psc) algorithm []. chemical shift regions containing spectral baseline noise or solvent signals […]

PMCID: 5299068
PMID: 28194448
DOI: 10.1128/mSphere.00005-17

[…] by presaturation. a spectral width of 16 ppm was used in each dimension., preprocessing and opls-da (orthogonal projections to latent structures discriminant analysis) were carried out with both mvapack () and software that was developed in our laboratory for a previous study () using the python programing language with numpy and scipy for calculations and matplotlib for visualization. […]


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MVAPACK institution(s)
Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA

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