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

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
Package: quantMSImageR
Title: Processing and Quantification of Targeted Mass Spectrometry Imaging
    Data
Version: 0.99.5
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'
    'contribution_hm.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'
    'stitch_acquisitions.R'
    'summarise_cal_levels.R'
    'trim_MSI.R'
    'validate.R'
    'zero2na.R'
Config/roxygen2/version: 8.0.0