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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 citations

 (65)
call_split

Application of metabolomics in prediction of lymph node metastasis in papillary thyroid carcinoma

2018
PLoS One
PMCID: 5839571
PMID: 29509799
DOI: 10.1371/journal.pone.0193883
call_split See protocol

[…] ea. 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 intensi […]

call_split

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
call_split See protocol

[…] 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 for furth […]

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

[…] recommend the removal of the upfield region (0.00–0.60 ppm), the residual water region (~ 4.50–4.9 ppm) and the urea region (5.5–6.1 ppm), especially prior to alignment and binning.We recommend that icoshift should be used in the alignment of biofluid (esp. urine) NMR spectra.No specific recommendation on the best spectral binning method is possible, although equidistant binning appears to be the […]

call_split

Evolution of the metabolome in response to selection for increased immunity in populations of Drosophila melanogaster

2017
PLoS One
PMCID: 5693281
PMID: 29149207
DOI: 10.1371/journal.pone.0188089
call_split See protocol

[…] The entire range of resonances in the 1D 1H NMR spectra was used without binning for the statistical analysis. Spectral data were converted into ASCII format and aligned using the Icoshift algorithm []. The spectral region between δ = 4.6 − 4.8 ppm was excluded from the analysis, to remove errors due to the residual water signal. Data were normalized to the total area, to be ab […]

library_books

Amyloid β42 peptide is toxic to non neural cells in Drosophila yielding a characteristic metabolite profile and the effect can be suppressed by PI3K

2017
PMCID: 5703620
PMID: 29141953
DOI: 10.1242/bio.029991

[…] d to the free-induction decay prior to Fourier transformation. All spectra were referenced to the TSP signal at −0.017 ppm, automatically phased and baseline corrected. The spectra were aligned using icoshift (). The spectra were normalized to total intensity in order to suppress separation based on variations in amount of sample. Metabolite assignments were done based on chemical shifts only, usi […]

library_books

PG Metrics: A chemometric based approach for classifying bacterial peptidoglycan data sets and uncovering their subjacent chemical variability

2017
PLoS One
PMCID: 5645090
PMID: 29040278
DOI: 10.1371/journal.pone.0186197

[…] The baseline corrected data sets are subjected to the icoshift algorithm by selecting the second simulated chromatogram as the reference. The icoshift analysis is performed on the entire range of the simulated chromatograms. The obtained results are show […]

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

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