AlpsNMR

This is the development version of AlpsNMR; for the stable release version, see AlpsNMR.

Automated spectraL Processing System for NMR

Bioconductor version: Development (3.21)

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] (ORCID: ), Francisco Madrid Gambin [aut] (ORCID: ), Luis Fernandez [aut] (ORCID: ), Laura López Sánchez [ctb], Héctor Gracia Cabrera [aut], Santiago Marco Colás [aut] (ORCID: ), Nestlé Institute of Health Sciences [cph], Institute for Bioengineering of Catalonia [cph], Miller Jack [ctb] (ORCID: , Autophase wrapper, ASICS export)

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

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("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

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

browseVignettes("AlpsNMR")

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	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Cheminformatics, Classification, DataImport, Metabolomics, Preprocessing, Software, Visualization
Version	4.9.0
In Bioconductor since	BioC 3.12 (R-4.0) (4 years)
License	MIT + file LICENSE
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)
System Requirements
URL	https://sipss.github.io/AlpsNMR/ https://github.com/sipss/AlpsNMR
Bug Reports	https://github.com/sipss/AlpsNMR/issues

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)
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report

Package Archives

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

Source Package	AlpsNMR_4.9.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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