Package: AlpsNMR
Type: Package
Title: Automated spectraL Processing System for NMR
Version: 4.11.0
Date: 2024-08-10
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
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: devel
git_last_commit: 487e98f
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-04 21:25:16 UTC; biocbuild
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 4.5.0; ; 2025-06-05 12:25:20 UTC; windows
