Package: CompoundDb 1.11.0

Johannes Rainer

CompoundDb: Creating and Using (Chemical) Compound Annotation Databases

CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.

Authors:Jan Stanstrup [aut], Johannes Rainer [aut, cre], Josep M. Badia [ctb], Roger Gine [aut], Andrea Vicini [aut], Prateek Arora [ctb]

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CompoundDb.pdf |CompoundDb.html✨
CompoundDb/json (API)
NEWS

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

Peer review:

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

On BioConductor:CompoundDb-1.9.5(bioc 3.20)CompoundDb-1.8.0(bioc 3.19)

massspectrometrymetabolomicsannotationdatabasesmass-spectrometry

8.23 score 16 stars 1 packages 49 scripts 482 downloads 59 exports 110 dependencies

Last updated 23 days agofrom:ef9eafc015. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winOKOct 30 2024
R-4.4-macOKOct 30 2024
R-4.3-winOKOct 30 2024
R-4.3-macOKOct 30 2024

Exports:backendInitializeCompDbcompound_tbl_lipidblastcompound_tbl_sdfCompoundIdFiltercompoundscompoundVariablescopyCompDbcreateCompDbcreateCompDbPackagedataStoragedbconndeleteCompounddeleteIondeleteSpectraemptyCompDbExactmassFilterexpandMzIntensityextractByIndexFormulaFilterhasMsMsSpectraimport_mona_sdfInchiFilterInchikeyFilterinsertCompoundinsertIoninsertSpectraintensity<-IonAdductFilterIonDbIonIdFilterIonMzFilterIonRtFilterionsionVariablesmake_metadatamass2mzmetadataMsBackendCompDbmsms_spectra_hmdbmsms_spectra_monaMsmsMzRangeMaxFilterMsmsMzRangeMinFiltermz<-NameFilterpeaksDatapeaksVariablesprecScanNumshowSpectraspectraDataspectraNamesspectraNames<-spectraVariablesSpectrumIdFiltersrc_compdbsupportedFilterstablestic

Dependencies:AnnotationFilteraskpassbase64encBHBiobaseBiocGenericsBiocParallelbitbit64bitopsblobbslibcachemChemmineRcliclueclustercodetoolscolorspacecpp11crosstalkcurlDBIdbplyrdigestdplyrDTevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixmemoiseMetaboCoreUtilsmgcvmimeMsCoreUtilsmunsellnlmeopensslpillarpkgconfigplogrpngpromisesProtGenericspurrrR6rappdirsRColorBrewerRcppRCurlrjsonrlangrmarkdownRSQLitersvgS4VectorssassscalessnowSpectrastringistringrsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunxml2XVectoryamlzlibbioc

Creating CompoundDb annotation resources

Rendered fromcreate-compounddb.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-05-29
Started: 2017-10-31

Usage of Annotation Resources with the CompoundDb Package

Rendered fromCompoundDb-usage.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-05-29
Started: 2020-10-23

Readme and manuals

Help Manual

Help pageTopics
Simple compound (metabolite) databasesCompDb CompDb-class compounds,CompDb-method compoundVariables compoundVariables,CompDb-method copyCompDb dbconn,CompDb-method deleteCompound deleteCompound,CompDb-method deleteCompound,IonDb-method deleteSpectra deleteSpectra,CompDb-method hasMsMsSpectra insertCompound insertCompound,CompDb-method insertSpectra insertSpectra,CompDb,Spectra-method mass2mz mass2mz,ANY-method mass2mz,CompDb-method metadata,CompDb-method show show,CompDb-method Spectra,CompDb-method spectraVariables,CompDb-method src_compdb supportedFilters,CompDb-method tables
Extract compound data from LipidBlastcompound_tbl_lipidblast
Extract compound data from a file in SDF formatcompound_tbl_sdf
Create a CompDb databasecreateCompDb createCompDbPackage emptyCompDb make_metadata
Expand m/z and intensity values in a data.frameexpandMzIntensity
Filters supported by CompDb and IonDbCompoundIdFilter CompoundIdFilter-class ExactmassFilter ExactmassFilter-class Filter-classes FormulaFilter FormulaFilter-class InchiFilter InchiFilter-class InchikeyFilter InchikeyFilter-class IonAdductFilter IonAdductFilter-class IonIdFilter IonIdFilter-class IonMzFilter IonMzFilter-class IonRtFilter IonRtFilter-class MsmsMzRangeMaxFilter MsmsMzRangeMaxFilter-class MsmsMzRangeMinFilter MsmsMzRangeMinFilter-class NameFilter NameFilter-class SpectrumIdFilter SpectrumIdFilter-class
Import compound and spectrum information from MoNaimport_mona_sdf
IonDb: compound database with additional ion informationdeleteIon deleteIon,IonDb-method insertIon insertIon,IonDb-method IonDb IonDb,character,CompDb-method IonDb,character,missing-method IonDb,CompDb,missing-method IonDb,DBIConnection,CompDb-method IonDb,DBIConnection,missing-method IonDb,missing,missing-method IonDb-class ions ions,IonDb-method ionVariables ionVariables,IonDb-method show,IonDb-method
CompDb-based MS spectrum backend$<-,MsBackendCompDb-method backendBpparam,MsBackendCompDb-method backendInitialize,MsBackendCompDb-method dataStorage,MsBackendCompDb-method extractByIndex,MsBackendCompDb,ANY-method intensity<-,MsBackendCompDb-method MsBackendCompDb MsBackendCompDb-class mz<-,MsBackendCompDb-method peaksData,MsBackendCompDb-method peaksVariables,MsBackendCompDb-method precScanNum,MsBackendCompDb-method show,MsBackendCompDb-method spectraData,MsBackendCompDb-method spectraNames,MsBackendCompDb-method spectraNames<-,MsBackendCompDb-method tic,MsBackendCompDb-method [,MsBackendCompDb,ANY-method
Import MS/MS spectra from HMDB xml filesmsms_spectra_hmdb
Import MS/MS spectra from MoNamsms_spectra_mona