AlpsNMR

DOI: 10.18129/B9.bioc.AlpsNMR    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see AlpsNMR.

Automated spectraL Processing System for NMR

Bioconductor version: 3.14

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 [aut], Sergio Oller Moreno [aut, cre] , Francisco Madrid Gambin [aut] , Luis Fernandez [aut] , Héctor Gracia Cabrera [aut], Santiago Marco Colás [aut] , Nestlé Institute of Health Sciences [cph], Institute for Bioengineering of Catalonia [cph]

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

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("AlpsNMR")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("AlpsNMR")

 

HTML	R Script	Introduction to AlpsNMR
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Cheminformatics, Classification, DataImport, Metabolomics, Preprocessing, Software, Visualization
Version	3.4.0
In Bioconductor since	BioC 3.12 (R-4.0) (1.5 years)
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
LinkingTo
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	AlpsNMR_3.4.0.tar.gz
Windows Binary	AlpsNMR_3.4.0.zip
macOS 10.13 (High Sierra)	AlpsNMR_3.4.0.tgz
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/
Package Downloads Report	Download Stats