DOI: 10.18129/B9.bioc.AlpsNMR    

This is the development version of AlpsNMR; for the stable release version, see AlpsNMR.

Automated spectraL Processing System for NMR

Bioconductor version: Development (3.15)

Reads Bruker NMR data directories both zipped and unzipped. It provides automated and efficient signal processing for untargeted NMR metabolomics. It is able to interpolate the samples, detect outliers, exclude regions, normalize, detect peaks, align the spectra, integrate peaks, manage metadata and visualize the spectra. After spectra proccessing, it can apply multivariate analysis on extracted data. Efficient plotting with 1-D data is also available. Basic reading of 1D ACD/Labs exported JDX samples is also available.

Author: Ivan Montoliu Roura <Ivan.MontoliuRoura at>, Sergio Oller Moreno <sergioller at>, Francisco Madrid Gambin <fmadrid at>, Luis Fernandez <lfernandez at>, Héctor Gracia Cabrera <hgracia at>, Santiago Marco Colás <smarco at>, Nestlé Institute of Health Sciences Montoliu Roura <Ivan.MontoliuRoura at>, Institute for Bioengineering of Catalonia Oller Moreno <sergioller at>

Maintainer: Sergio Oller Moreno <sergioller at>

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biocViews Cheminformatics, Classification, DataImport, Metabolomics, Preprocessing, Software, Visualization
Version 3.5.0
In Bioconductor since BioC 3.12 (R-4.0) (1 year)
License MIT + file LICENSE
Depends R (>= 4.0), dplyr (>= 0.7.5), future (>= 1.10.0), magrittr (>= 1.5)
Imports utils, graphics, stats, grDevices, signal (>= 0.7-6), assertthat (>= 0.2.0), rlang (>=, stringr (>= 1.3.1), tibble (>= 1.3.4), tidyr (>= 1.0.0), readxl (>= 1.1.0), plyr (>= 1.8.4), purrr (>= 0.2.5), glue (>= 1.2.0), reshape2 (>= 1.4.3), GGally (>= 1.4.0), mixOmics(>= 6.3.2), matrixStats (>= 0.54.0), writexl (>= 1.0), fs (>= 1.2.6), rmarkdown (>= 1.10), speaq (>= 2.4.0), htmltools (>= 0.3.6), ggrepel (>= 0.8.0), pcaPP (>= 1.9-73), furrr (>= 0.1.0), ggplot2 (>= 3.1.0), baseline (>= 1.2-1), zip (>= 2.0.4), tidyselect (>= 0.2.5), vctrs (>= 0.3.0), BiocParallel, SummarizedExperiment, S4Vectors
Suggests DT (>= 0.5), testthat (>= 2.0.0), plotly (>= 4.7.1), ChemoSpec, knitr
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