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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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No version available

Maintainer


  • person_outline MVAPACK

Publication for MVAPACK

MVAPACK citations

 (8)
library_books

Linking imaging to omics utilizing image guided tissue extraction

2018
Proc Natl Acad Sci U S A
PMCID: 5879681
PMID: 29507209
DOI: 10.1073/pnas.1718304115

[…] 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 spectra […]

library_books

Application of kernel principal component analysis and computational machine learning to exploration of metabolites strongly associated with diet

2018
Sci Rep
PMCID: 5821832
PMID: 29467421
DOI: 10.1038/s41598-018-20121-w

[…] profiling. 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, on […]

library_books

Recommended strategies for spectral processing and post processing of 1D 1H NMR data of biofluids with a particular focus on urine

2018
Metabolomics
PMCID: 5809546
PMID: 29479299
DOI: 10.1007/s11306-018-1321-4

[…] rces 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 Metabolom […]

library_books

Metabolic Investigations of the Molecular Mechanisms Associated with Parkinson’s Disease

2017
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 were rem […]

library_books

Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic Induced Disruptions

2017
PMCID: 5299068
PMID: 28194448
DOI: 10.1128/mSphere.00005-17

[…] ressed 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. The no […]

call_split

Metabolic reprogramming induced by ketone bodies diminishes pancreatic cancer cachexia

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

[…] pulse sequence to remove the solvent peak and maintain a flat baseline []. The spectra were collected at 300 K with 32 K data points, 128 scans, 16 dummy scans, and a spectral width of 5,483 Hz. Our MVAPACK software (http://bionmr.unl.edu/mvapack.php) [] was used to process the 1D 1H NMR spectra. The raw NMR data was only Fourier transformed and automatically phased. The resulting NMR spectrum wa […]

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

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