icoshift statistics

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icoshift specifications

Information


Unique identifier OMICS_06040
Name icoshift
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for icoshift

icoshift in pipeline

2013
PMCID: 3871890
PMID: 24251761
DOI: 10.1021/ac403111s

[…] fourier-transformed and phase corrected in nmrlab. spectra were then transferred to metabolab, and baseline correction was applied using common control points. analyte peaks were aligned using icoshift() and signals for background and internal controls were excluded. the spectra were normalized using pqn, mean-centered and variance-stabilized using pareto scaling. pca analyses were carried […]


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icoshift in publications

 (53)
PMCID: 5915433
PMID: 29691425
DOI: 10.1038/s41598-018-23954-7

[…] mestrenova version 7.1.0 to limit the effect of concentration differences between samples. minor chemical shifts due to ph alterations in tissue extracts and serum were adjusted and aligned using icoshift algorithm tool for matlab,. individual metabolites were manually identified based on expected chemical-shift and coupling-constant values obtained from various sources, including earlier […]

PMCID: 5839571
PMID: 29509799
DOI: 10.1371/journal.pone.0193883

[…] the spectral region between 0.5 and 10 ppm was divided into bins of 0.01 ppm width. the water region from 4.6 ppm to 4.9 ppm was excluded prior to analysis. the binned data were aligned using the icoshift algorithm in matlab [], and were converted to the simca-p format in excel. pareto scaling was used to preprocess the data. the intensity of each metabolite was normalized to the total […]

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

[…] collected 1h nmr data (32,000 data points) were normalized via probabilistic quotient normalization using the mqtl package (revolution r open software, 8.0.1 beta 64-bit) and aligned using the icoshift program on matlab r2015b (mathworks japan, tokyo, japan) in an in-house computing environment. peak-picked nmr data and icp-oes data were merged into a data matrix with auto scaling […]

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

[…] processes as correlation optimized warping (cow) (nielsen et al. ), fuzzy warping (wu et al. ), peak alignment by beam search (forshed et al. ; lee and woodruff ), and interval correlation shifting (icoshift) (savorani et al. ). these methods are known as pairwise alignment techniques because they align each nmr spectrum to a chosen reference nmr spectrum, one by one. the reference spectrum […]

PMCID: 5693281
PMID: 29149207
DOI: 10.1371/journal.pone.0188089

[…] have evolved over the course of several generations, we compared the unhandled control fly treatments (iu and su). we used the opls-da statistical approach on 1d nmr spectral data aligned using the icoshift algorithm [, ]. opls-da maximizes the covariance between the measured data and the response variable (nmr peak intensities and predictive classifications respectively). shows […]


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icoshift institution(s)
Institute for Health and Consumer Protection, Joint Resarch Centre, Ispra, Italy

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