Package: CompoundDb 1.9.4
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:
CompoundDb_1.9.4.tar.gz
CompoundDb_1.9.4.zip(r-4.5)CompoundDb_1.9.4.zip(r-4.4)CompoundDb_1.9.4.zip(r-4.3)
CompoundDb_1.9.4.tgz(r-4.4-any)CompoundDb_1.9.4.tgz(r-4.3-any)
CompoundDb_1.9.4.tar.gz(r-4.5-noble)CompoundDb_1.9.4.tar.gz(r-4.4-noble)
CompoundDb_1.9.4.tgz(r-4.4-emscripten)CompoundDb_1.9.4.tgz(r-4.3-emscripten)
CompoundDb.pdf |CompoundDb.html✨
CompoundDb/json (API)
NEWS
| # Install 'CompoundDb' in R: |
| install.packages('CompoundDb', repos = c('https://rformassspectrometry.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rformassspectrometry/compounddb/issues
On BioConductor:CompoundDb-1.9.4(bioc 3.20)CompoundDb-1.8.0(bioc 3.19)
massspectrometrymetabolomicsannotationdatabasesmass-spectrometry
Last updated 2 months agofrom:53c2f362a0. Checks:OK: 5 NOTE: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 12 2024 |
| R-4.5-win | NOTE | Sep 12 2024 |
| R-4.5-linux | NOTE | Sep 12 2024 |
| R-4.4-win | OK | Sep 12 2024 |
| R-4.4-mac | OK | Sep 12 2024 |
| R-4.3-win | OK | Aug 13 2024 |
| R-4.3-mac | OK | Aug 13 2024 |
Exports:backendInitializeCompDbcompound_tbl_lipidblastcompound_tbl_sdfCompoundIdFiltercompoundscompoundVariablescopyCompDbcreateCompDbcreateCompDbPackagedataStoragedbconndeleteCompounddeleteIondeleteSpectraemptyCompDbExactmassFilterexpandMzIntensityFormulaFilterhasMsMsSpectraimport_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 Sep 12 2024.Last update: 2024-05-29
Started: 2017-10-31
Usage of Annotation Resources with the CompoundDb Package
Rendered fromCompoundDb-usage.Rmdusingknitr::rmarkdownon Sep 12 2024.Last update: 2024-05-29
Started: 2020-10-23
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Simple compound (metabolite) databases | CompDb 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 LipidBlast | compound_tbl_lipidblast |
| Extract compound data from a file in SDF format | compound_tbl_sdf |
| Create a CompDb database | createCompDb createCompDbPackage emptyCompDb make_metadata |
| Expand m/z and intensity values in a data.frame | expandMzIntensity |
| Filters supported by CompDb and IonDb | CompoundIdFilter 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 MoNa | import_mona_sdf |
| IonDb: compound database with additional ion information | deleteIon 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 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 files | msms_spectra_hmdb |
| Import MS/MS spectra from MoNa | msms_spectra_mona |
