AlpsNMR

Automated spectraL Processing System for NMR

Bioconductor version: 3.23 · Package version: 4.14.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("AlpsNMR")

Details

Maintainer	Sergio Oller Moreno <sergioller@gmail.com>
Author	Ivan Montoliu Roura [aut], Sergio Oller Moreno [aut, cre] (ORCID: <https://orcid.org/0000-0002-8994-1549>), Francisco Madrid Gambin [aut] (ORCID: <https://orcid.org/0000-0001-9333-0014>), Luis Fernandez [aut] (ORCID: <https://orcid.org/0000-0001-9790-6287>), Laura López Sánchez [ctb], Héctor Gracia Cabrera [aut], Santiago Marco Colás [aut] (ORCID: <https://orcid.org/0000-0003-2663-2965>), Nestlé Institute of Health Sciences [cph], Institute for Bioengineering of Catalonia [cph], Miller Jack [ctb] (ORCID: <https://orcid.org/0000-0002-6258-1299>, Autophase wrapper, ASICS export)
License	MIT + file LICENSE
URL	https://sipss.github.io/AlpsNMR/, https://github.com/sipss/AlpsNMR
Bug Reports	https://github.com/sipss/AlpsNMR/issues
Downloads rank	334
Source branch	RELEASE_3_23
biocViews	Cheminformatics, Classification, DataImport, Metabolomics, Preprocessing, Software, Visualization

Documentation

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Source package

Dependencies

Depends: R (>= 4.2)

Imports: utils, generics, graphics, stats, grDevices, cli, magrittr (>= 1.5), dplyr (>= 1.1.0), signal (>= 0.7-6), rlang (>= 0.3.0.1), scales (>= 1.2.0), stringr (>= 1.3.1), tibble (>= 1.3.4), tidyr (>= 1.0.0), tidyselect, readxl (>= 1.1.0), purrr (>= 0.2.5), glue (>= 1.2.0), reshape2 (>= 1.4.3), mixOmics (>= 6.22.0), matrixStats (>= 0.54.0), fs (>= 1.2.6), rmarkdown (>= 1.10), speaq (>= 2.4.0), htmltools (>= 0.3.6), pcaPP (>= 1.9-73), ggplot2 (>= 3.1.0), baseline (>= 1.2-1), vctrs (>= 0.3.0), BiocParallel (>= 1.34.0)

Suggests: ASICS, BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5), GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr, NMRphasing, plotly (>= 4.7.1), progressr, SummarizedExperiment, S4Vectors, testthat (>= 2.0.0), writexl (>= 1.0), zip (>= 2.0.4)