AlpsNMR

DOI: 10.18129/B9.bioc.AlpsNMR    

Automated spectraL Processing System for NMR

Bioconductor version: Release (3.12)

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] , Francisco Madrid Gambin [aut] , Luis Fernandez [aut, cre] , Héctor Gracia Cabrera [aut], Nestlé Institute of Health Sciences [cph], Institute for Bioengineering of Catalonia [cph]

Maintainer: Luis Fernandez <lfernandez at ibecbarcelona.eu>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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 3.0.4
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License 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), BiocParallel, SummarizedExperiment, S4Vectors
LinkingTo
Suggests DT (>= 0.5), testthat (>= 2.0.0), plotly (>= 4.7.1), ChemoSpec, knitr
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Depends On Me
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Build Report  

Package Archives

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

Source Package AlpsNMR_3.0.4.tar.gz
Windows Binary AlpsNMR_3.0.4.zip
macOS 10.13 (High Sierra) AlpsNMR_3.0.4.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
Old Source Packages for BioC 3.12 Source Archive

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