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CompoundDb
This is thereleased version of CompoundDb; for the devel version, seeCompoundDb.
Creating and Using (Chemical) Compound Annotation Databases
Bioconductor version: Release (3.22)
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.
Author: Jan Stanstrup [aut]
ORCID: 0000-0003-0541-7369, Johannes Rainer [aut, cre] ORCID: 0000-0002-6977-7147, Josep M. Badia [ctb] ORCID: 0000-0002-5704-1124, Roger Gine [aut] ORCID: 0000-0003-0288-9619, Andrea Vicini [aut] ORCID: 0000-0001-9438-6909, Prateek Arora [ctb] ORCID: 0000-0003-0822-9240
Maintainer: Johannes Rainer <johannes.rainer at eurac.edu>
citation("CompoundDb")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("CompoundDb")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CompoundDb")| Creating CompoundDb annotation resources | HTML | R Script |
| Usage of Annotation Resources with the CompoundDb Package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation,MassSpectrometry,Metabolomics,Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1), methods,AnnotationFilter,S4Vectors |
| Imports | BiocGenerics,ChemmineR,tibble,jsonlite,dplyr,DBI,dbplyr,RSQLite,Biobase,ProtGenerics(>= 1.35.3),xml2,IRanges,Spectra(>= 1.15.10),MsCoreUtils,MetaboCoreUtils,BiocParallel,stringi |
| System Requirements | |
| URL | https://github.com/RforMassSpectrometry/CompoundDb |
| Bug Reports | https://github.com/RforMassSpectrometry/CompoundDb/issues |
See More
| Suggests | knitr,rmarkdown,testthat,BiocStyle(>= 2.5.19),MsBackendMgf |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | MetaboAnnotation,pubchem.bio |
| Suggests Me | AHMassBank,AnnotationHub |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | CompoundDb_1.14.0.tar.gz |
| Windows Binary (x86_64) | CompoundDb_1.14.0.zip |
| macOS Binary (x86_64) | CompoundDb_1.14.0.tgz |
| macOS Binary (arm64) | CompoundDb_1.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CompoundDb |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CompoundDb |
| Bioc Package Browser | https://code.bioconductor.org/browse/CompoundDb/ |
| Package Short Url | https://bioconductor.org/packages/CompoundDb/ |
| Package Downloads Report | Download Stats |