Package: IDSL.UFA 2.0

Dinesh Barupal

IDSL.UFA: United Formula Annotation (UFA) for HRMS Data Processing

A pipeline to annotate chromatography peaks from the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120> with molecular formulas of a prioritized chemical space using an isotopic profile matching approach. The 'IDSL.UFA' workflow only requires mass spectrometry level 1 (MS1) data for formula annotation. The 'IDSL.UFA' methods was described in <doi:10.1021/acs.analchem.2c00563> .

Authors:Sadjad Fakouri-Baygi [aut], Dinesh Barupal [cre, aut]

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IDSL.UFA.pdf |IDSL.UFA.html✨
IDSL.UFA/json (API)

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

Peer review:

Bug tracker:https://github.com/idslme/idsl.ufa/issues

On CRAN:

exposomeisotopic-distribution-calculationslipidomicsmass-spectrometrymetabolomicsmolecular-formulae-assignmentsmall-molecule

32 exports 7 stars 1.53 score 24 dependencies 1 dependents 1 scripts 294 downloads

Last updated 1 years agofrom:28dbcd67fd. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 01 2024
R-4.5-winOKSep 01 2024
R-4.5-linuxOKSep 01 2024
R-4.4-winOKSep 01 2024
R-4.4-macOKSep 01 2024
R-4.3-winOKSep 01 2024
R-4.3-macOKSep 01 2024

Exports:aggregatedIPdbListGeneratoraligned_molecular_formula_annotatordetect_formula_setselement_sorterextendedSENIORruleformula_adduct_calculatorformula_vector_generatorhill_molecular_formula_printeridentificationScoreCalculatorionization_pathway_deconvoluterisotopic_profile_calculatormolecular_formula_annotatormolecular_formula_elements_filtermolecular_formula_library_generatormolecular_formula_library_searchmolecularFormula2IPdbmonoisotopicMassCalculatorscoreCoefficientsEvaluationscoreCoefficientsOptimizationscoreCoefficientsReplicateUFA_enumerated_chemical_spaceUFA_enumerated_chemical_space_xlsxAnalyzerUFA_formula_sourceUFA_formula_source_xlsxAnalyzerUFA_IPdbMergerUFA_locate_regexUFA_PubChem_formula_extractionUFA_score_coefficients_correctorUFA_score_function_optimizationUFA_score_function_optimization_xlsxAnalyzerUFA_workflowUFA_xlsxAnalyzer

Dependencies:base64enccellrangerclicpp11crayonfansigluehmsIDSL.IPAIDSL.MXPlifecyclemagrittrpillarpkgconfigprettyunitsprogressR6readxlrematchrlangtibbleutf8vctrsxml2

Readme and manuals

Help Manual

Help pageTopics
aggregatedIPdbListGeneratoraggregatedIPdbListGenerator
Aligned Molecular Formula Annotatoraligned_molecular_formula_annotator
Organic Class Detection by Repeated Unit Patternsdetect_formula_sets
Element Sorterelement_sorter
extended SENIOR rule checkextendedSENIORrule
Formula Adduct Calculatorformula_adduct_calculator
Molecular Formula Vector Generatorformula_vector_generator
Print Hill Molecular Formulahill_molecular_formula_printer
Multiplicative Identification Score for the IDSL.UFA pipelineidentificationScoreCalculator
Ionization Pathway Deconvoluterionization_pathway_deconvoluter
Isotopic Profile Calculatorisotopic_profile_calculator
Molecular Formula Annotatormolecular_formula_annotator
molecular_formula_elements_filtermolecular_formula_elements_filter
Molecular Formula Database Producermolecular_formula_library_generator
Molecular Formula Library Searchmolecular_formula_library_search
Molecular Formula to IPDBmolecularFormula2IPdb
Monoisotopic Mass CalculatormonoisotopicMassCalculator
Score Coefficient EvaluationscoreCoefficientsEvaluation
Coefficients Score OptimizationscoreCoefficientsOptimization
Zero Score FunctionscoreCoefficientsReplicate
IPDBs from UFA Enumerated Chemical Space (ECS) approachUFA_enumerated_chemical_space
IPDBs from UFA Enumerated Chemical Space (ECS) xlsx AnalyzerUFA_enumerated_chemical_space_xlsxAnalyzer
IPDB from a Molecular Formulas SourceUFA_formula_source
UFA Formula Source xlsxAnalyzerUFA_formula_source_xlsxAnalyzer
UFA IPDB MergerUFA_IPdbMerger
UFA Locate regexUFA_locate_regex
UFA PubChem Formula ExtractionUFA_PubChem_formula_extraction
Score Coefficients Corrector for MolecularFormulaAnnotationTableUFA_score_coefficients_corrector
UFA Score Coefficient WorkflowUFA_score_function_optimization
UFA Score Optimization xlsx AnalyzerUFA_score_function_optimization_xlsxAnalyzer
UFA WorkflowUFA_workflow
UFA xlsx AnalyzerUFA_xlsxAnalyzer