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 (3.22)

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, MassSpectrometry, Metabolomics, Software
Version	1.13.0
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

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_1.13.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)	CompoundDb_1.13.0.tgz
macOS Binary (arm64)	CompoundDb_1.13.0.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