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.
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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
6.25 score 3 stars 1 dependents 71 scripts
tima - Taxonomically Informed Metabolite Annotation
TIMA provides a reproducible workflow for taxonomically informed metabolite annotation from feature tables, MS/MS spectra, and optional external resources such as 'SIRIUS' and 'GNPS' outputs. It combines mass, spectral, taxonomic, and structural evidence into a transparent scoring framework that can be inspected step-by-step. The package targets metabolomics practitioners who need configurable, scriptable, and documented annotation pipelines for research and production settings.
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edam:topic_3172edam:topic_0154edam:topic_2258edam:topic_0637edam:topic_3370edam:topic_0769edam:operation_3803edam:operation_3801edam:operation_3214edam:operation_3629edam:operation_3460edam:operation_3927edam:format_3681edam:format_3651edam:format_1196edam:format_1199metaboliteannotationchemotaxonomyscoringsystemnaturalproductscomputationalmetabolomicstaxonomicdistancespecializedmetabolomelc-msmsmetabolite-annotationmetabolomicsnatural-productsscoring-systemspecialized-metabolometaxonomyquarto
6.23 score 17 stars 44 scripts
SpectraToQueries - Spectra to queries
Translates tandem mass spectrometry (MS/MS) spectral libraries into diagnostic fragment and neutral-loss ion queries for chemical structure and skeleton classification, ranked by Matthews Correlation Coefficient (MCC).
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mass-spectrometrymetabolomicscheminformaticsnatural-productsspectral-analysisdiagnostic-ionsquery-generationedam:topic_3172edam:topic_0154edam:topic_3370edam:topic_2258edam:topic_0780edam:operation_3214edam:operation_3803edam:operation_4074edam:operation_3629edam:operation_3695edam:operation_2990edam:operation_0224edam:data_2536edam:data_0943edam:data_0962edam:data_2048edam:format_3651edam:format_3475knowledge-extractionmonoterpene-indole-alkaloidsquerying-systemspectral-informationspectral-librarytandem-ms
3.49 score 2 stars 1 scripts
CentroidR - Centroid Profile Mass Spectrometry Data
CentroidR provides the infrastructure to centroid profile mass spectrometry spectra (mzML) with independent MS1 and MS2 tolerances, valley-based peak splitting, and intensity-weighted m/z aggregation.
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centroidingspectramass-spectrometrymetabolomicslipidomicsmzmledam:topic_3172edam:topic_0153edam:topic_0154edam:topic_3370edam:operation_3215edam:operation_3214edam:operation_3695edam:data_0943edam:data_2536edam:format_3244centroidmass-spectra
3.24 score
sapid - A Strategy to Analyze Plant Extracts Taste in Depth
Provides the infrastructure to implement a Strategy to Analyze Plant Extracts Taste In Depth (SAPID) by combining sensory panel profiling, projective napping, and Ascending Forced Choice (AFC) threshold testing with untargeted LC-MS feature tables, Charged Aerosol Detection (CAD) semi-quantification, taxonomically informed metabolite annotations (TIMA), and 1D proton NMR spectral clustering.
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computationalmetabolomicsnaturalextractstastesensoryanalysismassspectrometrynmrspectroscopyedam:topic_3172edam:topic_0154edam:topic_3370edam:topic_2258edam:topic_0780edam:topic_0593edam:topic_0092edam:topic_2269edam:operation_3803edam:operation_3214edam:operation_3215edam:operation_3432edam:operation_3465edam:operation_2428edam:operation_0337edam:operation_3203edam:operation_2942edam:operation_3925edam:data_2536edam:data_3488edam:data_2048edam:format_3244edam:format_3475edam:format_3752edam:format_3508lc-msmsmetabolomicsnatural-extracts
3.23 score
EthnoBotaPhyWR - Infrastructure for Ethnobotanical and Phytochemical Data Integration with Wikidata
Infrastructure and curated ethnobotanical and phytochemical datasets for analyzing plant families, including phylogenetic integration and visualization tools. Includes vendored functions from the 'cascade' package (https://github.com/adafede/cascade) to minimize the dependency tree.
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ethnobotanyphytochemistrytaxonomywikidatanaturalproductschemotaxonomyphylogeneticsedam:topic_0780edam:topic_0154edam:topic_2258edam:topic_3293edam:topic_0637edam:topic_3077edam:operation_0224edam:operation_2422edam:operation_2990edam:operation_0324edam:operation_0567edam:operation_0337edam:operation_1812edam:data_0872edam:data_3272edam:data_1872edam:data_1868edam:data_3028edam:data_1463edam:data_2301edam:data_1086edam:format_1196edam:format_1199edam:format_3475edam:format_3508edam:format_3604
3.13 score 6 scripts