Protocols

speaq specifications

Information


Unique identifier OMICS_13687
Name speaq
Alternative name spectrum alignment and quantitation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Apache License version 2.0
Computer skills Advanced
Version 2.3.3
Stability Stable
Requirements
stats, parallel, grid, graphics, utils, grDevices, ggplot2, data.table, rmarkdown, knitr, gridBase, cluster, reshape2, foreach, xml2, gridExtra, R(≥3.1.0), doSNOW, impute, datasets, MassSpecWavelet, mQTL, rvest, missForest
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Trung Nghia Vu
  • person_outline Charlie Beirnaert

Additional information


https://github.com/nghiavtr/speaq

Publications for spectrum alignment and quantitation

speaq citations

 (2)
call_split

Prediction and modeling of pre analytical sampling errors as a strategy to improve plasma NMR metabolomics data

2017
Bioinformatics
PMCID: 5870544
PMID: 29036400
DOI: 10.1093/bioinformatics/btx442
call_split See protocol

[…] Processed 1D NMR data were imported into R v 3.2.0 (), aligned using the ‘speaq’ R package v 1.2.1 (), and shift-normalized to TSP at δ = 0. Metabolic features (n = 478) were obtained using continuous wavelet transformation peak picking and extracting peak heights at corres […]

call_split

Non invasive urinary metabolomic profiling discriminates prostate cancer from benign prostatic hyperplasia

2017
Metabolomics
PMCID: 5533870
PMID: 28804274
DOI: 10.1007/s11306-017-1194-y
call_split See protocol

[…] –5.52 ppm) regions were excluded from the analysis to avoid interferences arising from differences in water suppression and variability from urea signal, respectively. Spectra were aligned using the “Speaq” R package, a hierarchical cluster-based peak alignment algorithm that minimizes chemical shift variations (Vu et al. ), and normalization of the aligned spectra was performed according to the p […]

speaq institution(s)
Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Natural Products & Food Research and Analysis (NatuRA), Department of Pharmaceutical Sciences, University of Antwerp, Wilrijk, Belgium; Toxicological Center, Department of Pharmaceutical Sciences, University of Antwerp, Wilrijk, Belgium
speaq funding source(s)
Supported by a GOA (Geconcentreerde Onderzoeksactie) from the University 377 of Antwerp.

speaq reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review speaq