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CompoundDb

This is the development version of CompoundDb; for the stable release version, see CompoundDb.

Creating and Using (Chemical) Compound Annotation Databases


Bioconductor version: Development (3.19)

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 (from within R, enter citation("CompoundDb")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews Annotation, MassSpectrometry, Metabolomics, Software
Version 1.7.1
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, AnnotationHub
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CompoundDb_1.7.1.tar.gz
Windows Binary CompoundDb_1.7.1.zip
macOS Binary (x86_64) CompoundDb_1.7.1.tgz
macOS Binary (arm64) CompoundDb_1.7.1.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