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
VignetteBuilder: quarto
biocViews: metaboliteAnnotation, chargedAerosolDetector,
        semiQuantitative, naturalProducts, computationalMetabolomics,
        specializedMetabolome
X-schema.org-keywords: metaboliteAnnotation, chargedAerosolDetector,
        semiQuantitative, naturalProducts, computationalMetabolomics,
        specializedMetabolome
Config/pak/sysreqs: cmake libglpk-dev make libarchive-dev libicu-dev
        libpng-dev libuv1-dev libxml2-dev libnetcdf-dev libssl-dev
        python3 libnode-dev zlib1g-dev
Repository: https://adafede.r-universe.dev
Date/Publication: 2026-07-03 08:36:43 UTC
RemoteUrl: https://github.com/adafede/cascade
RemoteRef: main
RemoteSha: e45648162b323feb4e87406070282c4a38637598
NeedsCompilation: no
Packaged: 2026-07-05 14:25:04 UTC; root
Author: Adriano Rutz [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0443-9902>)