quantMSImageR/DESCRIPTION at main · MJS-708/quantMSImageR · GitHub

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Package: quantMSImageR
Title: Processing and Quantification of Targeted Mass Spectrometry Imaging
    Data
Version: 0.99.7
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'
    'alignFeatures.R'
    'applySNR.R'
    'back2NA.R'
    'bindPanels.R'
    'buildFeatureMeta.R'
    'combineMSIs.R'
    'contributionHm.R'
    'createCalCurve.R'
    'createMSIDataMatrix.R'
    'generateTxtImages.R'
    'imageR.R'
    'int2SNR.R'
    'int2conc.R'
    'int2response.R'
    'join_ion_library.R'
    'palettes.R'
    'plotCalCoverage.R'
    'quantMSImageR-package.R'
    'quantileHm.R'
    'readMRM.R'
    'removeBlankMzs.R'
    'runExample.R'
    'runStudy.R'
    'selectTissuePixels.R'
    'stitchAcquisitions.R'
    'summariseCalLevels.R'
    'trimMSI.R'
    'validate.R'
    'zero2NA.R'
Config/roxygen2/version: 8.0.0