AlpsNMR
Automated spectraL Processing System for NMR
Bioconductor version: 3.24 · Package version: 4.15.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("AlpsNMR")Details
| Maintainer | Sergio Oller Moreno <sergioller@gmail.com> |
| Author | Ivan Montoliu Roura [aut], Sergio Oller Moreno [aut, cre] (ORCID: <https://orcid.org/0000-0002-8994-1549>), Francisco Madrid Gambin [aut] (ORCID: <https://orcid.org/0000-0001-9333-0014>), Luis Fernandez [aut] (ORCID: <https://orcid.org/0000-0001-9790-6287>), Laura López Sánchez [ctb], Héctor Gracia Cabrera [aut], Santiago Marco Colás [aut] (ORCID: <https://orcid.org/0000-0003-2663-2965>), Nestlé Institute of Health Sciences [cph], Institute for Bioengineering of Catalonia [cph], Miller Jack [ctb] (ORCID: <https://orcid.org/0000-0002-6258-1299>, Autophase wrapper, ASICS export) |
| License | MIT + file LICENSE |
| URL | https://sipss.github.io/AlpsNMR/, https://github.com/sipss/AlpsNMR |
| Bug Reports | https://github.com/sipss/AlpsNMR/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Cheminformatics, Classification, DataImport, Metabolomics, Preprocessing, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/AlpsNMR/ |
Citation
From within R, enter citation("AlpsNMR"):
Ivan Montoliu Roura, Sergio Oller Moreno, Francisco Madrid Gambin, Luis Fernandez, Héctor Gracia Cabrera, Santiago Marco Colás. AlpsNMR: Automated spectraL Processing System for NMR. doi:10.18129/B9.bioc.AlpsNMR, R package version 4.15.0, https://bioconductor.org/packages/AlpsNMR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | AlpsNMR_4.15.0.tar.gz |
| Windows binary (x86_64) | AlpsNMR_4.15.0.zip |
| macOS binary (arm64) | AlpsNMR_4.15.0.tgz |
| macOS binary (x86_64) | AlpsNMR_4.15.0.tgz |
Dependencies
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)
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)