AlpsNMR

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

Maintainer: Sergio Oller Moreno <sergioller at gmail.com>

Citation (from within R, enter citation("AlpsNMR")):

Installation

To install this package, start R (version "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("AlpsNMR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

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 (>= 0.3.0.1), 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
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Suggests DT (>= 0.5), testthat (>= 2.0.0), plotly (>= 4.7.1), ChemoSpec, knitr
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Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/AlpsNMR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/AlpsNMR
Package Short Url https://bioconductor.org/packages/AlpsNMR/
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