AlpsNMR
Automated spectraL Processing System for NMR
Bioconductor version: Release (3.20)
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]
Maintainer: Sergio Oller Moreno <sergioller at gmail.com>
, 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], Miller Jack [ctb] (citation("AlpsNMR")):
Installation
To install this package, start R (version "4.4") 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) | R Script | |
| Vignette 01: Introduction to AlpsNMR (start here) | R Script | |
| Vignette 02: Handling metadata and annotations | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Cheminformatics, Classification, DataImport, Metabolomics, Preprocessing, Software, Visualization |
| Version | 4.8.0 |
| 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 |
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 | |
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| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | AlpsNMR_4.8.0.tar.gz |
| Windows Binary (x86_64) | AlpsNMR_4.8.0.zip |
| macOS Binary (x86_64) | AlpsNMR_4.8.0.tgz |
| macOS Binary (arm64) | AlpsNMR_4.8.0.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 |