Package: MRManalyzeR
Type: Package
Title: Process and Analyse Targeted LC-MS Lipidomics and Metabolomics
        Data
Version: 0.99.0
Authors@R: person("Matthew J.", "Smith",
                  email = "mattyjsmith123@gmail.com",
                  role = c("aut", "cre"),
                  comment = c(ORCID = "0000-0002-7357-2670"))
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, normalisation, internal-standard and volume
        adjustment of vendor-reported concentrations, missing-value
        imputation and batch correction. Each step is an exported
        function acting on a struct DatasetExperiment; a complete
        workflow can additionally be driven from a single YAML
        configuration via run_MRManalyzeR(), 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: magrittr, dplyr, tidyr, tibble, yaml, openxlsx, janitor,
        rmarkdown, methods, ggplot2, rlang, grDevices, pheatmap
Suggests: ggrepel, plotly, DT, htmltools, knitr, cowplot, gridExtra,
        BiocStyle, testthat (>= 3.0.0), withr
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://biocstaging.r-universe.dev
Date/Publication: 2026-07-22 15:53:00 UTC
RemoteUrl: https://github.com/BiocStaging/MRManalyzeR
RemoteRef: HEAD
RemoteSha: 5e00a87a8b3e948c3998aa23953087eefd06e632
NeedsCompilation: no
Packaged: 2026-07-22 16:13:35 UTC; root
Author: Matthew J. Smith [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-7357-2670>)
Maintainer: Matthew J. Smith <mattyjsmith123@gmail.com>