Package: notame
Type: Package
Title: Workflow for non-targeted LC-MS metabolic profiling
Version: 1.2.0
Authors@R: c(
    person("Anton", "Klåvus", role = c("aut", "cph"),
           comment = c(ORCID = "0000-0003-2612-0230")),
    person("Jussi", "Paananen", role = c("aut", "cph"),
           comment = c(ORCID = "0000-0001-5100-4907")),
    person("Oskari", "Timonen", role = c("aut", "cph"),
           comment = c(ORCID = "0000-0002-6317-6260")),
    person("Atte", "Lihtamo", role = "aut"),
    person("Vilhelm", "Suksi", email = "vksuks@utu.fi", role = c("aut", "cre"),
           comment = c(ORCID = "0009-0005-1108-518X")),
    person("Retu", "Haikonen", role = "aut",
           comment = c(ORCID = "0000-0003-0830-3850")),
    person("Leo", "Lahti", role = "aut",
           comment = c(ORCID = "0000-0001-5537-637X")),
    person("Kati", "Hanhineva", role = "aut",
           comment = c(ORCID = "0000-0001-6834-7375")),
    person("Ville", "Koistinen", role = "ctb",
           comment = c(ORCID = "0000-0003-1587-8361")),
    person("Olli", "Kärkkäinen", role = "ctb",
           comment = c(ORCID = "0000-0003-0825-4956")),
    person("Artur", "Sannikov", role = "ctb",
           comment = c(ORCID = "0000-0001-7765-123X")))
Description: Provides functionality for untargeted LC-MS metabolomics research as specified in the associated protocol article in the 'Metabolomics Data Processing and Data Analysis—Current Best Practices' special issue of the Metabolites journal (2020). This includes tabular data preprocessing and quality control, uni- and multivariate analysis as well as quality control visualizations, feature-wise visualizations and results visualizations. Raw data preprocessing and functionality related to biological context, such as pathway analysis, is not included.
License: MIT + file LICENSE
Encoding: UTF-8
biocViews: BiomedicalInformatics, Metabolomics, DataImport,
        MassSpectrometry, BatchEffect, MultipleComparison,
        Normalization, QualityControl, Visualization, Preprocessing
Depends: R (>= 4.5.0), ggplot2, SummarizedExperiment
Imports: BiocGenerics, BiocParallel, dplyr, futile.logger, methods,
        openxlsx, S4Vectors, scales, stringr, tidyr, utils
Suggests: BiocStyle, fpc, igraph, knitr, missForest, notameViz,
        notameStats, pcaMethods, RUVSeq, testthat
URL: https://github.com/hanhineva-lab/notame,
        https://hanhineva-lab.github.io/notame/
BugReports: https://github.com/hanhineva-lab/notame/issues
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Config/testthat/parallel: true
git_url: https://git.bioconductor.org/packages/notame
git_branch: RELEASE_3_23
git_last_commit: c06d914
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
NeedsCompilation: no
Packaged: 2026-04-28 23:39:35 UTC; biocbuild
Author: Anton Klåvus [aut, cph] (ORCID:
    <https://orcid.org/0000-0003-2612-0230>),
  Jussi Paananen [aut, cph] (ORCID:
    <https://orcid.org/0000-0001-5100-4907>),
  Oskari Timonen [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-6317-6260>),
  Atte Lihtamo [aut],
  Vilhelm Suksi [aut, cre] (ORCID:
    <https://orcid.org/0009-0005-1108-518X>),
  Retu Haikonen [aut] (ORCID: <https://orcid.org/0000-0003-0830-3850>),
  Leo Lahti [aut] (ORCID: <https://orcid.org/0000-0001-5537-637X>),
  Kati Hanhineva [aut] (ORCID: <https://orcid.org/0000-0001-6834-7375>),
  Ville Koistinen [ctb] (ORCID: <https://orcid.org/0000-0003-1587-8361>),
  Olli Kärkkäinen [ctb] (ORCID: <https://orcid.org/0000-0003-0825-4956>),
  Artur Sannikov [ctb] (ORCID: <https://orcid.org/0000-0001-7765-123X>)
Maintainer: Vilhelm Suksi <vksuks@utu.fi>
