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AlpsNMR

Automated spectraL Processing System for NMR


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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")
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

Details

biocViews Cheminformatics, Classification, DataImport, Metabolomics, Preprocessing, Software, Visualization
Version 4.4.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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(>= 6.22.0), 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
System Requirements
URL https://sipss.github.io/AlpsNMR/ https://github.com/sipss/AlpsNMR
Bug Reports https://github.com/sipss/AlpsNMR/issues
See More
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)
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Package Archives

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

Source Package AlpsNMR_4.4.0.tar.gz
Windows Binary AlpsNMR_4.4.0.zip
macOS Binary (x86_64) AlpsNMR_4.4.0.tgz
macOS Binary (arm64) AlpsNMR_4.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/AlpsNMR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/AlpsNMR
Bioc Package Browser https://code.bioconductor.org/browse/AlpsNMR/
Package Short Url https://bioconductor.org/packages/AlpsNMR/
Package Downloads Report Download Stats