Pre-requisites | More details
Package: cascade 0.0.0.9002
cascade: Contextualizing Untargeted Annotation with Semi-Quantitative Charged Aerosol Detection for Pertinent Characterization of Natural Extracts
Provides the infrastructure to perform Automated Composition Assessment of Natural Extracts by combining untargeted mass spectrometry feature tables and taxonomically informed metabolite annotations (TIMA) with semi-quantitative universal detectors such as Charged Aerosol Detection (CAD) and Photodiode Array (PDA) chromatograms. Includes Fourier filtering, derivative-based peak sharpening, peak integration, extracted ion chromatogram correlation, Wikidata/LOTUS chemotaxonomic literature queries, and interactive visualizations.
Authors:
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
metaboliteannotationchargedaerosoldetectorsemiquantitativenaturalproductscomputationalmetabolomicsspecializedmetabolomeedam:topic_3172edam:topic_0154edam:topic_3370edam:topic_2258edam:topic_0780edam:operation_3803edam:operation_3214edam:operation_3215edam:operation_3628edam:operation_3799edam:operation_3203edam:operation_2942edam:format_3244edam:format_3475edam:format_2331edam:format_3790charged-aerosol-detectorchemical-compositionlc-msmsmetabolite-annotationmetabolomicsnatural-extractsnatural-productsquarto
Last updated from:f3b0c7fd3c (on main). Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 294 | ||
| source / vignettes | OK | 255 | ||
| linux-release | OK | 372 | ||
| macos-release | OK | 437 | ||
| macos-oldrel | OK | 414 | ||
| windows-devel | OK | 297 | ||
| windows-release | OK | 269 | ||
| windows-oldrel | OK | 277 | ||
| wasm-release | OK | 155 |
Exports:check_chromatograms_alignmentcheck_peaks_integrationgenerate_idsgenerate_pseudochromatogramsgenerate_tablesplot_timaprepare_tima_annotationsprocess_compare_peaksquery_wikidatataxon_name_to_qid
Dependencies:askpassbase64encbaselinebigDBiobaseBiocGenericsbiocmakebitopsbslibcachemclicommonmarkcpp11crosstalkcurldata.tabledigestdir.expirydplyrevaluatefarverfastmapfilelockfontawesomefsgenericsggplot2gluegtgtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonlitejuicyjuiceknitrlabelinglaterlazyevallifecyclelitedownmagrittrmarkdownmemoisemimemzRncdf4opensslotelpillarpkgconfigplotlypromisesProtGenericspurrrR6rappdirsRColorBrewerRcppreactablereactRRhdf5librlangrmarkdownS7sassscalesSparseMstringistringrsystibbletidyrtidyselecttinytexutf8V8vctrsviridisLitewithrxfunxml2yaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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 |
| Check multi-detector chromatogram alignment | check_chromatograms_alignment |
| Check chromatographic peak detection and integration bounds | check_peaks_integration |
| Generate chemotaxonomic literature hierarchies and plots from Wikidata/LOTUS | generate_ids |
| Generate annotated pseudochromatograms and chemical class treemaps | generate_pseudochromatograms |
| Generate interactive HTML and TSV summary tables of annotated peaks | generate_tables |
| Plot TIMA annotation chemical class distributions | plot_tima |
| Prepare TIMA structural and predicted annotation tables | prepare_tima_annotations |
| Compare MS extracted ion chromatograms against detector peaks | process_compare_peaks |
| Query a SPARQL endpoint efficiently | query_wikidata |
| Convert a scientific taxon name to its Wikidata QID | taxon_name_to_qid |