Package: cascade 0.0.0.9000

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 [aut, cre]

cascade_0.0.0.9000.tar.gz
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cascade_0.0.0.9000.tgz(r-4.4-any)cascade_0.0.0.9000.tgz(r-4.3-any)
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cascade.pdf |cascade.html✨
cascade/json (API)
NEWS

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

Peer review:

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

On CRAN:

metabolite annotationcharged aerosol detectorsemi-quantitativenatural productscomputational metabolomicsspecialized metabolome

5.25 score 2 stars 63 scripts 7 exports 198 dependencies

Last updated 6 hours agofrom:ea17a73f41 (on main). Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-winNOTENov 22 2024
R-4.5-linuxNOTENov 22 2024
R-4.4-winNOTENov 22 2024
R-4.4-macNOTENov 22 2024
R-4.3-winNOTENov 22 2024
R-4.3-macNOTENov 22 2024

Exports:check_chromatograms_alignmentcheck_peaks_integrationgenerate_idsgenerate_pseudochromatogramsgenerate_tablesprocess_compare_peakstaxon_name_to_qid

Dependencies:abindaffyaffyioAnnotationFilterapeaskpassassertthatbackportsbase64encbase64urlbaselineBHbigDBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbitbit64bitopsbslibcachemcallrcaToolsclicliprclueclustercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDelayedArraydigestdocoptdoParalleldplyrDTevaluatefansifarverfastmapfontawesomeforcatsforeachformatRfsfstfstcorefurrrfutile.loggerfutile.optionsfuturegenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2globalsgluegtgtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphimputeIRangesisobanditeratorsjquerylibjsonlitejuicyjuiceknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalimSolvelistenvlpSolvemagrittrMALDIquantmarkdownMASSMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmgcvmimeMsBackendMgfMsBackendMspMsCoreUtilsmsentropyMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmeopensslparallellypcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprocessxprogressprogressrpromisesProtGenericspsPSMatchpurrrQFeaturesquadprogR.methodsS3R.ooR.utilsR6rappdirsratelimitrRColorBrewerRcppreactablereactRreadrrentrezreshape2rexRhdf5librlangrmarkdownrnclrotlS4ArraysS4VectorssassscalessecretbaseshinyshinybusyshinyWidgetssnowsourcetoolsSparseArraySparseMSpectrastatmodstringistringrSummarizedExperimentsystargetstibbletidyfsttidyrtidyselecttidytabletimatinytextzdbUCSC.utilsutf8V8vctrsviridisLitevisNetworkvroomvsnWikidataQueryServiceRWikipediRwithrxfunXMLxml2xtableXVectoryamlzlibbioc

General comments about the use of CASCADE

Adriano Rutz

Rendered fromcascade.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-11-21
Started: 2024-11-04

Readme and manuals

Help Manual

Help pageTopics
Add chromato lineadd_chromato_line
Baseline chromatogrambaseline_chromatogram
Change intensity namechange_intensity_name
Check chromatogramscheck_chromatograms
Check chromatograms alignmentcheck_chromatograms_alignment
Check export dircheck_export_dir
Check chromatograms alignmentcheck_peaks_integration
Compare peakscompare_peaks
Derivderiv
Extract chromatogramextract_chromatogram
Extract MS peakextract_ms_peak
Extract MS progressextract_ms_progress
Filter FFTfilter_fft
Temp GT functionformat_gt
Generate IDsgenerate_ids
Generate pseudochromatogramsgenerate_pseudochromatograms
Generate IDsgenerate_tables
Get peaksget_peaks
Hierarchies grouped progresshierarchies_grouped_progress
Hierarchies Progresshierarchies_progress
Histograms progresshistograms_progress
Improve signalimprove_signal
Improve signals progressimprove_signals_progress
Join peaksjoin_peaks
Keep best candidateskeep_best_candidates
Load annotationsload_annotations
Load chromatogramsload_chromatograms
Load featuresload_features
Load features informedload_features_informed
Load features not informedload_features_not_informed
Load MS dataload_ms_data
Load nameload_name
Make chromatographiablemake_chromatographiable
Make confidentmake_confident
Make no stereomake_no_stereo
Make othermake_other
Middle ptsmiddle_pts
Molinfomolinfo
No otherno_other
Normalize chromatonormalize_chromato
Normalize chromatograms listnormalize_chromatograms_list
P ACN Ip_acn_i
Peaks progresspeaks_progress
Plot chromatogramplot_chromatogram
Plot histogramsplot_histograms
Plot histograms confidentplot_histograms_confident
Plot histograms littplot_histograms_litt
Plot histograms taxoplot_histograms_taxo
Plot peak detectionplot_peak_detection
Plot results 1plot_results_1
Plot results 2plot_results_2
Predict responsepredict_response
Prehistograms progressprehistograms_progress
Prepare comparisonprepare_comparison
Prepare featuresprepare_features
Prepare hierarchyprepare_hierarchy
Prepare mzprepare_mz
Prepare peaksprepare_peaks
Prepare plotprepare_plot
Prepare plot 2prepare_plot_2
Prepare rtprepare_rt
Preprocess chromatogramspreprocess_chromatograms
Preprocess peakspreprocess_peaks
Process compare peaksprocess_compare_peaks
Queries progressqueries_progress
Save histograms progresssave_histograms_progress
Save treemaps progresssave_treemaps_progress
Second dersecond_der
Signal sharpeningsignal_sharpening
Tables progresstables_progress
Taxon name to QIDtaxon_name_to_qid
Transform MStransform_ms
Treemaps progresstreemaps_progress
Treemaps progress no titletreemaps_progress_no_title
Wiki progresswiki_progress
Y as NAy_as_na