CompoundDb
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see CompoundDb.
Creating and Using (Chemical) Compound Annotation Databases
Bioconductor version: 3.17
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] 
, Johannes Rainer [aut, cre] , Josep M. Badia [ctb] , Roger Gine [aut] , Andrea Vicini [aut]
Maintainer: Johannes Rainer <johannes.rainer at eurac.edu>
citation("CompoundDb")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CompoundDb")
For older versions of R, please refer to the appropriate Bioconductor 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 | 1.4.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1), methods, AnnotationFilter, S4Vectors |
| Imports | BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics, xml2, IRanges, Spectra(>= 1.9.12), MsCoreUtils, MetaboCoreUtils, BiocParallel |
| 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 |
| Suggests Me | AHMassBank |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CompoundDb_1.4.0.tar.gz |
| Windows Binary | CompoundDb_1.4.0.zip |
| macOS Binary (x86_64) | CompoundDb_1.4.0.tgz |
| macOS Binary (arm64) | CompoundDb_1.4.0.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 |
| Old Source Packages for BioC 3.17 | Source Archive |