CompoundDb

This is the released version of CompoundDb; for the devel version, see CompoundDb.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15

Creating and Using (Chemical) Compound Annotation Databases

Bioconductor version: Release (3.23)

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")):

Jan Stanstrup, Johannes Rainer, Roger Gine, Andrea Vicini. CompoundDb: Creating and Using (Chemical) Compound Annotation Databases. doi:10.18129/B9.bioc.CompoundDb, R package version 1.16.0, https://bioconductor.org/packages/CompoundDb.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

Usage of Annotation Resources with the CompoundDb Package	HTML	R Script
Creating CompoundDb annotation resources	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, MassSpectrometry, Metabolomics, Software
Version	1.16.0
In Bioconductor since	BioC 3.15 (R-4.2) (4.5 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, data.table
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, pubchem.bio
Suggests Me	AHMassBank, AnnotationHub, MetMashR
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	CompoundDb_1.16.0.tar.gz
Windows Binary (x86_64)	CompoundDb_1.16.0.zip
macOS Binary (big-sur-x86_64)	CompoundDb_1.16.0.tgz
macOS Binary (sonoma-arm64)	CompoundDb_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CompoundDb
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CompoundDb
Package Short Url	https://bioconductor.org/packages/CompoundDb/
Package Downloads Report	Download Stats