Package: MRManalyzeR
Type: Package
Title: Process and Analyse Targeted LC-MS Lipidomics and Metabolomics
        Data
Version: 0.99.8
Authors@R: c(
    person("Matthew J.", "Smith",
           email = "mattyjsmith123@gmail.com",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-7357-2670")),
    person("Antonio", "Checa",
           role = "aut",
           comment = c(ORCID = "0000-0002-0674-3329")))
Description: Reproducible post-acquisition processing of targeted LC-MS/MS
    lipidomics and metabolomics results exported from Waters TargetLynx or
    from Skyline, or supplied as a plain sample-by-analyte matrix. Reads the
    quantitative result tables, integrates them with sample and feature
    metadata, and applies configurable signal filtering (SNR, LOD or LOQ),
    blank filtering, batch correction, normalisation, internal-standard and
    volume adjustment of vendor-reported concentrations, and missing-value
    imputation. Each step is an exported function acting on a struct
    DatasetExperiment; a complete workflow can additionally be driven from a
    single YAML configuration via runMRManalyzeR(), which also renders
    self-contained HTML data-quality and statistical reports. Chromatographic
    peak detection, peak integration and calibration-curve fitting from raw
    mass-spectrometry data are outside its scope.
License: MIT + file LICENSE
Encoding: UTF-8
biocViews: Metabolomics, Lipidomics, MassSpectrometry, QualityControl,
        Normalization, BatchEffect, Visualization, WorkflowStep
URL: https://github.com/MJS-708/MRManalyzeR
BugReports: https://github.com/MJS-708/MRManalyzeR/issues
Depends: R (>= 4.5.0), struct
Imports: dplyr, tidyr, tibble, yaml, openxlsx, janitor, rmarkdown,
        methods, ggplot2, ggnewscale, rlang, grDevices, pheatmap,
        withr, DT, stats, utils
Suggests: pmp, structToolbox, pls, SummarizedExperiment, ggrepel,
        plotly, htmltools, knitr, cowplot, gridExtra, BiocStyle,
        testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
git_url: https://git.bioconductor.org/packages/MRManalyzeR
git_branch: devel
git_last_commit: 15a43ca
git_last_commit_date: 2026-11-05
Repository: Bioconductor 3.24
Date/Publication: 2026-11-06
NeedsCompilation: no
Packaged: 2026-11-07 00:24:01 UTC; biocbuild
Author: Matthew J. Smith [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-7357-2670>),
  Antonio Checa [aut] (ORCID: <https://orcid.org/0000-0002-0674-3329>)
Maintainer: Matthew J. Smith <mattyjsmith123@gmail.com>
