cascade/DESCRIPTION at main · Adafede/cascade · 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
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
Package: cascade
Title: Contextualizing untargeted Annotation with Semi-quantitative Charged Aerosol Detection for pertinent characterization of natural Extracts
Version: 0.0.0.9002
Authors@R: c(
    person(given = "Adriano",
           family = "Rutz",
           email = "adafede@gmail.com",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-0443-9902"))
  )
Maintainer: Adriano Rutz <adafede@gmail.com>
Description: This package provides the infrastructure to perform
    Automated Composition Assessment of Natural Extracts.
License: AGPL (>= 3)
URL: https://github.com/adafede/cascade, https://adafede.github.io/cascade
BugReports: https://github.com/adafede/cascade/issues
Depends:
    R (>= 4.5.0)
Imports:
    baseline (>= 1.3.7),
    BiocParallel (>= 1.44.0),
    caTools (>= 1.18.3),
    curl (>= 7.1.0),
    data.table (>= 1.18.4),
    forcats (>= 1.0.1),
    ggplot2 (>= 4.0.3),
    gt (>= 1.3.0),
    htmltools (>= 0.5.9),
    httr2 (>= 1.2.2),
    MSnbase (>= 2.36.0),
    mzR (>= 2.44.0),
    plotly (>= 4.12.0),
    purrr (>= 1.2.2),
    R.utils (>= 2.13.0),
    stringi (>= 1.8.7),
    tibble (>= 3.3.1),
    tidytable (>= 0.11.2),
    tima (>= 2.13.0),
    utils
Remotes:
    taxonomicallyinformedannotation/tima
Suggests:
    altdoc (>= 0.7.2),
    BiocManager (>= 1.30.27),
    BiocVersion (>= 3.22.0),
    grateful (>= 0.3.0),
    knitr (>= 1.51),
    pkgload (>= 1.4.0),
    quarto (>= 1.5.1),
    lifecycle (>= 1.0.5),
    spelling,
    svglite (>= 2.2.2),
    testthat (>= 3.3.2)
ByteCompile: TRUE
Collate:
    'normalize_chromatograms_list.R'
    'add_chromato_line.R'
    'baseline_chromatogram.R'
    'cascade-package.R'
    'change_intensity_name.R'
    'check_chromatograms.R'
    'load_chromatograms.R'
    'deriv.R'
    'middle_pts.R'
    'second_der.R'
    'signal_sharpening.R'
    'filter_fft.R'
    'improve_signal.R'
    'extract_chromatogram.R'
    'check_chromatograms_alignment.R'
    'check_export_dir.R'
    'prepare_rt.R'
    'prepare_peaks.R'
    'prepare_mz.R'
    'get_peaks.R'
    'peaks_progress.R'
    'normalize_chromato.R'
    'join_peaks.R'
    'preprocess_peaks.R'
    'improve_signals_progress.R'
    'preprocess_chromatograms.R'
    'prepare_features.R'
    'plot_peak_detection.R'
    'load_name.R'
    'load_features.R'
    'check_peaks_integration.R'
    'colors.R'
    'compare_peaks.R'
    'correct_acn.R'
    'extract_ms_peak.R'
    'extract_ms_progress.R'
    'format_gt.R'
    'wiki_progress.R'
    'treemaps_progress.R'
    'taxon_name_to_qid.R'
    'tables_progress.R'
    'queries_progress.R'
    'prepare_plot.R'
    'prepare_hierarchy.R'
    'plot_histograms.R'
    'make_no_stereo.R'
    'make_chromatographiable.R'
    'hierarchies_grouped_progress.R'
    'hierarchies_progress.R'
    'generate_ids.R'
    'prepare_comparison.R'
    'no_other.R'
    'make_other.R'
    'plot_results.R'
    'make_confident.R'
    'y_as_na.R'
    'keep_best_candidates.R'
    'generate_pseudochromatograms.R'
    'molinfo.R'
    'load_features_informed.R'
    'load_annotations.R'
    'generate_tables.R'
    'globals.R'
    'histograms_progress.R'
    'load_features_not_informed.R'
    'load_ms_data.R'
    'plot_chromatogram.R'
    'plot_tima.R'
    'prehistograms_progress.R'
    'prepare_tima_annotations.R'
    'transform_ms.R'
    'process_compare_peaks.R'
    'query_wikidata.R'
    'save_histograms_progress.R'
    'save_treemaps_progress.R'
Config/roxygen2/markdown: TRUE
Config/roxygen2/version: 8.0.0
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
LazyData: TRUE
VignetteBuilder:
    quarto
biocViews: metaboliteAnnotation, chargedAerosolDetector, semiQuantitative, naturalProducts, computationalMetabolomics, specializedMetabolome
X-schema.org-keywords: metaboliteAnnotation, chargedAerosolDetector, semiQuantitative, naturalProducts, computationalMetabolomics, specializedMetabolome