DESCRIPTION

Package: quantMSImageR
Title: Quantification of Mass Spectrometry Imaging Data
Version: 0.2.0.0
Authors@R:
    person("Matthew", "Smith", , "mattyjsmith123@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-7357-2670"))
Description: Software tools (largely extended from the R package Cardinal) for
    quantification of mass spectrometry imaging (MSI) data, including
    signal-to-noise filtering, tissue fold-change computation, quantile
    heatmaps, and batch export of per-feature text images for external viewers.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends:
    R (>= 4.4.1),
    Cardinal (>= 3.6.2),
    dplyr (>= 1.1.4),
    ggplot2 (>= 4.0.0),
    tibble (>= 3.2.1),
    tidyr (>= 1.3.1)
Imports:
    ProtGenerics,
    chemCal (>= 0.2.3),
    viridis (>= 0.6.5),
    ggthemes (>= 5.1.0),
    scales (>= 1.3.0),
    DT (>= 0.33),
    magick (>= 2.8.4),
    ComplexHeatmap (>= 2.0.0),
    matrixStats (>= 0.63.0),
    pracma (>= 2.4.0),
    rmarkdown (>= 2.20),
    yaml (>= 2.3.0),
    patchwork (>= 1.2.0),
    htmltools (>= 0.5.0),
    purrr (>= 1.0.0),
    matter (>= 2.0.0),
    CardinalIO (>= 1.0.0),
    openxlsx (>= 4.2.0)
Suggests:
    testthat (>= 3.0.0),
    knitr (>= 1.40),
    rstudioapi (>= 0.15.0)
VignetteBuilder: knitr
Collate:
    'setClasses.R'
    'align_features.R'
    'applySNR.R'
    'back2NA.R'
    'bind_panels.R'
    'bind_polarities.R'
    'build_feature_meta.R'
    'read_mrm.R'
    'combine_MSI_features.R'
    'combine_MSIs.R'
    'combine_rds.R'
    'createMSIDatamatrix.R'
    'create_cal_curve.R'
    'extdata.R'
    'generate_txt_images.R'
    'ggplot_themes.R'
    'imageR.R'
    'int2conc.R'
    'int2response.R'
    'int2snr.R'
    'quantile_hm.R'
    'read_mrm_combined.R'
    'remove_blank_mzs.R'
    'run_example.R'
    'select_tissue_pixels.R'
    'setCommonAxis.R'
    'summarise_cal_levels.R'
    'trim_MSI.R'
    'zero2na.R'