Package: MetaboCoreUtils 1.20.1

Johannes Rainer

MetaboCoreUtils: Core Utils for Metabolomics Data

MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound mass-to-charge ratios and masses or functions to work with chemical formulas. The package provides also a set of adduct definitions and information on some commercially available internal standard mixes commonly used in MS experiments.

Authors:Johannes Rainer [aut, cre], Michael Witting [aut], Andrea Vicini [aut], Liesa Salzer [ctb], Sebastian Gibb [aut], Michael Stravs [ctb], Roger Gine [aut], William Kumler [aut], Philippine Louail [aut], Gabriele Tomè [aut]

MetaboCoreUtils_1.20.1.tar.gz
MetaboCoreUtils_1.20.1.zip(r-4.7)MetaboCoreUtils_1.20.1.zip(r-4.6)MetaboCoreUtils_1.20.1.zip(r-4.5)
MetaboCoreUtils_1.20.1.tgz(r-4.6-any)MetaboCoreUtils_1.20.1.tgz(r-4.5-any)
MetaboCoreUtils_1.20.1.tar.gz(r-4.7-any)MetaboCoreUtils_1.20.1.tar.gz(r-4.6-any)
MetaboCoreUtils_1.20.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MetaboCoreUtils/json (API)
NEWS

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

Bug tracker:https://github.com/rformassspectrometry/metabocoreutils/issues

On BioConductor:MetaboCoreUtils-1.21.1(bioc 3.24)MetaboCoreUtils-1.20.1(bioc 3.23)

infrastructuremetabolomicsmassspectrometrymass-spectrometry

10.22 score 9 stars 65 packages 91 scripts 3.8k downloads 40 exports 17 dependencies

Last updated from:ae5c09690b (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE141
linux-devel-x86_64OK182
source / vignettesOK216
linux-release-x86_64OK153
macos-release-arm64OK89
macos-oldrel-arm64OK86
windows-develOK116
windows-releaseOK116
windows-oldrelOK130
wasm-releaseOK123

Exports:addElementsadductFormulaadductNamesadductsadjust_lmbetaValuescalculateKmcalculateKmdcalculateMasscalculateRkmdcontainsElementsconvertMtimecorrectRindexcountElementsfit_lmformula2mzguessSourceindexRtimeinternalStandardMixNamesinternalStandardsisotopicSubstitutionMatrixisotopologuesisRkmdmass2mzmclosestmultiplyElementsmz2massnameMappingpasteElementspercentMissingrowBlankrowDratiorowPercentMissingrowRsdrsdsoftwareMappingsoftwareMappingSchemastandardizeFormulasubtractElementstranslate

Dependencies:BHBiocGenericsBiocParallelclueclustercodetoolscpp11formatRfutile.loggerfutile.optionsgenericslambda.rMASSMsCoreUtilsRcppS4Vectorssnow

Core Utils for Metabolomics Data

Rendered fromMetaboCoreUtils.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2024-04-13
Started: 2021-01-25

Readme and manuals

Help Manual

Help pageTopics
Combine chemical formulaeaddElements
Calculate a table of adduct (ionic) formulasadductFormula
Retrieve names of supported adductsadductNames adducts
Peak shape quality: beta parametersbetaValues
Kendrick mass defectscalculateKendrickMass calculateKm calculateKmd calculateRkmd isRkmd
Calculate exact masscalculateMass
Check if one formula is contained in anothercontainsElements
Convert migration times to effective mobilityconvertMtime
2-point correction of RIscorrectRindex
Count elements in a chemical formulacountElements
Linear model-based normalization of abundance matricesadjust_lm fit_lm
Calculate mass-to-charge ratio from a formulaformula2mz
Guess the source of namesguessSource
Convert retention times to retention indicesindexRtime
Get names of internal standard mixes provided by the packageinternalStandardMixNames
Get definitions for internal standardsinternalStandards
Definitions of isotopic substitutionsisotopicSubstitutionMatrix
Identfying isotopologue peaks in MS dataisotopologues
Calculate mass-to-charge ratiomass2mz
Extract closest values in a pairwise manner between two matricesmclosest
Multiply chemical formulas by a scalarmultiplyElements
Calculate neutral massmz2mass
Get mapping vector between two softwarenameMapping
Create chemical formula from a named vectorpasteElements
Basic quality assessment functions for metabolomicspercentMissing quality_assessment rowBlank rowDratio rowPercentMissing rowRsd rsd
Get supported software for name translationsoftwareMapping
Get mapping schema for name translationsoftwareMappingSchema
Standardize a chemical formulastandardizeFormula
subtract two chemical formulasubtractElements
Translate names based on a provided mappingtranslate