Package: quantMSImageR
Title: Processing and Quantification of Targeted Mass Spectrometry
        Imaging Data
Version: 0.99.0
Authors@R: 
    person("Matthew J.", "Smith", , "mattyjsmith123@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-7357-2670"))
Description: Implements tools for processing and quantifying targeted
        DESI-MRM mass spectrometry imaging (MSI) datasets, extending
        the Cardinal package. Includes signal-to-noise filtering
        against background pixels, tissue/background separation,
        per-feature ion images, quantile heatmaps, quantification
        against on-slide or on-tissue calibration standards, and batch
        export of per-feature text images for external viewers.
License: MIT + file LICENSE
URL: https://mjs-708.github.io/quantMSImageR,
        https://github.com/MJS-708/quantMSImageR
BugReports: https://github.com/MJS-708/quantMSImageR/issues
biocViews: Software, MassSpectrometry, ImagingMassSpectrometry,
        Metabolomics, Lipidomics, QualityControl, Normalization,
        Visualization
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.5.0), Cardinal (>= 3.6.2)
Imports: methods, stats, utils, grDevices, grid, chemCal (>= 0.2.3),
        viridis (>= 0.6.5), ComplexHeatmap (>= 2.20.0), circlize (>=
        0.4.15), matrixStats (>= 0.63.0), pracma (>= 2.4.0), rmarkdown
        (>= 2.20), purrr (>= 1.0.0), CardinalIO (>= 1.0.0),
        ProtGenerics (>= 1.34.0), dplyr (>= 1.1.4), ggplot2 (>= 4.0.0),
        tibble (>= 3.2.1), tidyr (>= 1.3.1), patchwork (>= 1.2.0), yaml
        (>= 2.3.0)
Suggests: testthat (>= 3.0.0), knitr (>= 1.40), BiocStyle (>= 2.28.0),
        rstudioapi (>= 0.15.0), DT (>= 0.33), htmltools (>= 0.5.0),
        magick (>= 2.8.4), openxlsx (>= 4.2.0), matter (>= 2.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Collate: 'setClasses.R' 'accessors.R' 'align_features.R' 'applySNR.R'
        'back2NA.R' 'bind_panels.R' 'build_feature_meta.R'
        'combine_MSIs.R' 'createMSIDatamatrix.R' 'create_cal_curve.R'
        'generate_txt_images.R' 'imageR.R' 'int2conc.R'
        'int2response.R' 'int2snr.R' 'join_ion_library.R' 'palettes.R'
        'plot_cal_coverage.R' 'quantMSImageR-package.R' 'quantile_hm.R'
        'read_mrm.R' 'remove_blank_mzs.R' 'run_example.R' 'run_study.R'
        'select_tissue_pixels.R' 'summarise_cal_levels.R' 'trim_MSI.R'
        'validate.R' 'zero2na.R'
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libuv1-dev perl
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-07-23 17:04:48 UTC
RemoteUrl: https://github.com/BiocStaging/quantMSImageR
RemoteRef: HEAD
RemoteSha: 8be881d9e298069154b9d4bf39caf59e68d27c08
NeedsCompilation: no
Packaged: 2026-07-23 18:56:29 UTC; root
Author: Matthew J. Smith [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-7357-2670>)
Maintainer: Matthew J. Smith <mattyjsmith123@gmail.com>