AlpsNMR

DOI: 10.18129/B9.bioc.AlpsNMR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see AlpsNMR.

Automated spectraL Processing System for NMR

Bioconductor version: 3.16

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] , Laura López Sánchez [ctb], 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 "4.2") 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")

 

PDF	R Script	Older Introduction to AlpsNMR (soft-deprecated API)
PDF	R Script	Vignette 01: Introduction to AlpsNMR (start here)
PDF	R Script	Vignette 02: Handling metadata and annotations
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Cheminformatics, Classification, DataImport, Metabolomics, Preprocessing, Software, Visualization
Version	4.0.4
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.2), future (>= 1.10.0)
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(>= 6.3.2), 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
LinkingTo
Suggests	BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5), GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr, plotly (>= 4.7.1), progressr, SummarizedExperiment, S4Vectors, testthat (>= 2.0.0), writexl (>= 1.0), zip (>= 2.0.4)
SystemRequirements
Enhances
URL	https://sipss.github.io/AlpsNMR/ https://github.com/sipss/AlpsNMR
BugReports	https://github.com/sipss/AlpsNMR/issues
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	AlpsNMR_4.0.4.tar.gz
Windows Binary	AlpsNMR_4.0.4.zip
macOS Binary (x86_64)	AlpsNMR_4.0.4.tgz
macOS Binary (arm64)	AlpsNMR_4.0.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/AlpsNMR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/AlpsNMR
Bioc Package Browser	https://code.bioconductor.org/browse/AlpsNMR/
Package Short Url	https://bioconductor.org/packages/AlpsNMR/
Package Downloads Report	Download Stats