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
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libssl-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-11-05 13:24:58 UTC
RemoteUrl: https://github.com/bioc/MRManalyzeR
RemoteRef: HEAD
RemoteSha: 15a43ca65d84ead4e947bcb3de22991740469859
NeedsCompilation: no
Packaged: 2026-11-06 00:35:17 UTC; root
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>