CompoundDb

Creating and Using (Chemical) Compound Annotation Databases

Bioconductor version: Release (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 (from within R, enter 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	PDF
NEWS	Text

Details

biocViews	Annotation, MassSpectrometry, Metabolomics, Software
Version	1.4.0
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 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
Linking To
Suggests	knitr, rmarkdown, testthat, BiocStyle(>= 2.5.19), MsBackendMgf
System Requirements
Enhances
URL	https://github.com/RforMassSpectrometry/CompoundDb
Bug Reports	https://github.com/RforMassSpectrometry/CompoundDb/issues

Depends On Me
Imports Me	MetaboAnnotation
Suggests Me	AHMassBank
Links To Me
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