CompoundDb

DOI:10.18129/B9.bioc.CompoundDb

Creating and Using (Chemical) Compound Annotation Databases

Bioconductor version: Release (3.16)

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

Installation

To install this package, start R (version "4.2") and enter:

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

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("CompoundDb")

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

Details

biocViews	Annotation,MassSpectrometry,Metabolomics,Software
Version	1.2.1
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 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(>= 1.5.17),MsCoreUtils,MetaboCoreUtils
LinkingTo
Suggests	knitr,rmarkdown,testthat,BiocStyle(>= 2.5.19),MsBackendMgf
SystemRequirements
Enhances
URL	https://github.com/RforMassSpectrometry/CompoundDb
BugReports	https://github.com/RforMassSpectrometry/CompoundDb/issues
Depends On Me
Imports Me	MetaboAnnotation
Suggests Me
Links To Me
Build Report

Package Archives

Followbob 体育网址 instructions to use this package in your R session.

Source Package	CompoundDb_1.2.1.tar.gz
Windows Binary	CompoundDb_1.2.1.zip
macOS Binary (x86_64)	CompoundDb_1.2.1.tgz
macOS Binary (arm64)	CompoundDb_1.2.1.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	//www.anjoumacpherson.com/packages/CompoundDb/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive