Package: cascade 0.0.0.9002

cascade: Contextualizing untargeted Annotation with Semi-quantitative Charged Aerosol Detection for pertinent characterization of natural Extracts

This package provides the infrastructure to perform Automated Composition Assessment of Natural Extracts.

Authors:Adriano Rutz

cascade_0.0.0.9002.tar.gz
cascade_0.0.0.9002.zip(r-4.7-any)cascade_0.0.0.9002.zip(r-4.6-any)cascade_0.0.0.9002.zip(r-4.5-any)
cascade_0.0.0.9002.tgz(r-4.6-any)cascade_0.0.0.9002.tgz(r-4.5-any)
cascade_0.0.0.9002.tar.gz(r-4.7-any)cascade_0.0.0.9002.tar.gz(r-4.6-any)
cascade_0.0.0.9002.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cascade/json (API)

# Install 'cascade' in R:

install.packages('cascade', repos = c('https://adafede.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adafede/cascade/issues

Pkgdown/docs site:https://adafede.github.io

Datasets:

cascade_annotations - CASCADE Example Datasets
cascade_chromatograms_negative - CASCADE Example Datasets
cascade_chromatograms_positive - CASCADE Example Datasets
cascade_features - CASCADE Example Datasets
cascade_features_informed - CASCADE Example Datasets
cascade_features_not_informed - CASCADE Example Datasets
cascade_ms_data - CASCADE Example Datasets

On CRAN:

metaboliteannotation chargedaerosoldetector semiquantitative naturalproducts computationalmetabolomics specializedmetabolome charged-aerosol-detector chemical-composition lc-msms metabolite-annotation metabolomics natural-extracts natural-products quarto

6.36 score 4 stars 1 packages 61 scripts 10 exports 147 dependencies

Last updated from:77cdf2a2e9 (on main). Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	487
source / vignettes	OK	451
linux-release	OK	511
macos-release	OK	494
macos-oldrel	OK	354
windows-devel	OK	486
windows-release	OK	483
windows-oldrel	OK	500
wasm-release	OK	244

Exports:check_chromatograms_alignment check_peaks_integration generate_ids generate_pseudochromatograms generate_tables plot_tima prepare_tima_annotations process_compare_peaks query_wikidata taxon_name_to_qid

Dependencies:abind affy affyio AnnotationFilter askpass base64enc baseline BH bigD Biobase BiocBaseUtils BiocGenerics biocmake BiocManager BiocParallel bitops bslib cachem caTools cli clue cluster codetools commonmark cpp11 crosstalk curl data.table DelayedArray digest dir.expiry doParallel dplyr evaluate farver fastmap filelock fontawesome forcats foreach formatR fs futile.logger futile.options generics GenomicRanges ggplot2 glue gt gtable highr htmltools htmlwidgets httr httr2 igraph impute IRanges isoband iterators jquerylib jsonlite juicyjuice knitr labeling lambda.r later lattice lazyeval lifecycle limma litedown magrittr MALDIquant markdown MASS Matrix MatrixGenerics matrixStats memoise MetaboCoreUtils mime MsCoreUtils MSnbase MultiAssayExperiment mzID mzR ncdf4 openssl otel pcaMethods pillar pkgconfig plotly plyr preprocessCore promises ProtGenerics PSMatch PTMods purrr QFeatures R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp reactable reactR reshape2 Rhdf5lib rlang rmarkdown S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray SparseM Spectra statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tidytable tima tinytex utf8 V8 vctrs viridisLite vsn withr xfun XML xml2 XVector yaml

General comments about the use of CASCADE

Pre-requisites | More details

Rendered fromcascade.qmdusingquarto::html

Last update: 2026-07-25
Started: 2024-11-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add chromato line	add_chromato_line
Baseline chromatogram	baseline_chromatogram
CASCADE Example Datasets	cascade_annotations cascade_chromatograms_negative cascade_chromatograms_positive cascade_datasets cascade_features cascade_features_informed cascade_features_not_informed cascade_ms_data
Change intensity name	change_intensity_name
Check chromatograms	check_chromatograms
Check chromatograms alignment	check_chromatograms_alignment
Check export dir	check_export_dir
Check chromatograms alignment	check_peaks_integration
Compare peaks	compare_peaks
Deriv	deriv
Extract chromatogram	extract_chromatogram
Extract MS peak	extract_ms_peak
Extract MS progress	extract_ms_progress
Filter FFT	filter_fft
Generate IDs	generate_ids
Generate pseudochromatograms	generate_pseudochromatograms
Generate IDs	generate_tables
Get peaks	get_peaks
Hierarchies grouped progress	hierarchies_grouped_progress
Hierarchies Progress	hierarchies_progress
Improve signal	improve_signal
Improve signals progress	improve_signals_progress
Join peaks	join_peaks
Keep best candidates	keep_best_candidates
Load annotations	load_annotations
Load chromatograms	load_chromatograms
Load features	load_features
Load features informed	load_features_informed
Load features not informed	load_features_not_informed
Load MS data	load_ms_data
Load name	load_name
Make chromatographiable	make_chromatographiable
Make confident	make_confident
Make no stereo	make_no_stereo
Make other	make_other
Middle pts	middle_pts
Molinfo	molinfo
No other	no_other
Normalize chromato	normalize_chromato
Normalize chromatograms list	normalize_chromatograms_list
P ACN I	p_acn_i
Peaks progress	peaks_progress
Plot histograms	plot_histograms
Plot histograms confident	plot_histograms_confident
Plot histograms litt	plot_histograms_litt
Plot histograms taxo	plot_histograms_taxo
Plot peak detection	plot_peak_detection
Plot results 1	plot_results_1
Plot TIMA	plot_tima
Prepare comparison	prepare_comparison
Prepare features	prepare_features
Prepare hierarchy	prepare_hierarchy
Prepare mz	prepare_mz
Prepare peaks	prepare_peaks
Prepare plot	prepare_plot
Prepare plot 2	prepare_plot_2
Prepare rt	prepare_rt
Prepare TIMA annotations	prepare_tima_annotations
Preprocess chromatograms	preprocess_chromatograms
Preprocess peaks	preprocess_peaks
Process compare peaks	process_compare_peaks
Queries progress	queries_progress
Query a SPARQL endpoint efficiently	query_wikidata
Second der	second_der
Signal sharpening	signal_sharpening
Tables progress	tables_progress
Taxon name to QID	taxon_name_to_qid
Transform MS	transform_ms
Treemaps progress no title	treemaps_progress_no_title
Wiki progress	wiki_progress
Y as NA	y_as_na