Package: AlpsNMR
Type: Package
Title: Automated spectraL Processing System for NMR
Version: 4.12.0
Date: 2025-09-24
Encoding: UTF-8
Authors@R: c(
    person(given = "Ivan",
           family = "Montoliu Roura",
           email = "Ivan.MontoliuRoura@rd.nestle.com",
           role = c("aut")),
    person(given = "Sergio",
           family = "Oller Moreno",
           email = "sergioller@gmail.com",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-8994-1549")),
    person(given = "Francisco",
           family = "Madrid Gambin",
           email = "fmadrid@ibecbarcelona.eu",
           role = c("aut"),
           comment = c(ORCID = "0000-0001-9333-0014")),
    person(given = "Luis",
           family = "Fernandez",
           email = "lfernandez@ibecbarcelona.eu",
           role = c("aut"),
           comment = c(ORCID = "0000-0001-9790-6287")),
    person(given = "Laura",
           family = "López Sánchez",
           role = c("ctb")),
    person(given = "Héctor",
           family = "Gracia Cabrera",
           email = "hgracia@ibecbarcelona.eu",
           role = c("aut")),
    person(given = "Santiago",
           family = "Marco Colás",
           email = "smarco@ibecbarcelona.eu",
           role = c("aut"),
           comment = c(ORCID = "0000-0003-2663-2965")),
    person(given = "Nestlé Institute of Health Sciences",
           role = "cph"),
    person(given = "Institute for Bioengineering of Catalonia",
           role = "cph"),
    person(given = "Miller",
           family = "Jack",
           email = "jack.miller@physics.org", 
           role=c("ctb"),
           comment = c(ORCID = "0000-0002-6258-1299", "Autophase wrapper, ASICS export"))
    )
Description: 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.
License: MIT + file LICENSE
URL: https://sipss.github.io/AlpsNMR/, https://github.com/sipss/AlpsNMR
BugReports: https://github.com/sipss/AlpsNMR/issues
LazyData: FALSE
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)
biocViews: Software, Preprocessing, Visualization, Classification,
        Cheminformatics, Metabolomics, DataImport
RoxygenNote: 7.3.1
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
Config/pak/sysreqs: libfreetype6-dev libglpk-dev libglu1-mesa-dev make
        texlive libicu-dev libpng-dev libxml2-dev libgl1-mesa-dev
        libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:04:39 UTC
RemoteUrl: https://github.com/bioc/AlpsNMR
RemoteRef: RELEASE_3_22
RemoteSha: a1d41e5525065cd5eb655927a25ff145625f5b0f
NeedsCompilation: no
Packaged: 2026-01-29 08:28:05 UTC; root
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)
Maintainer: Sergio Oller Moreno <sergioller@gmail.com>
Built: R 4.5.2; ; 2026-01-29 08:30:02 UTC; windows
