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Bioconductor - AlpsNMR (development version)

AlpsNMR

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

Automated spectraL Processing System for NMR

Bioconductor version: Development (3.22)

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: 0000-0002-8994-1549 , Francisco Madrid Gambin [aut] ORCID: 0000-0001-9333-0014 , Luis Fernandez [aut] ORCID: 0000-0001-9790-6287 , Laura LÃ³pez SÃ¡nchez [ctb], HÃ©ctor Gracia Cabrera [aut], Santiago Marco ColÃ¡s [aut] ORCID: 0000-0003-2663-2965 , NestlÃ© Institute of Health Sciences [cph], Institute for Bioengineering of Catalonia [cph], Miller Jack [ctb] (ORCID: ORCID: 0000-0002-6258-1299 , 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 Details biocViews Cheminformatics, Classification, DataImport, Metabolomics, Preprocessing, Software, Visualization Version 4.11.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 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 See More 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 Suggests Me Links To Me Build Report Build Report Package Archives

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

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