biodb

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13

Biodb, a Library and a Development Framework for Connecting to Chemical and Biological Databases

Bioconductor version: Release (3.23)

The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.

Author: Pierrick Roger [aut, cre] ORCID: 0000-0001-8177-4873 , Alexis Delabrière [ctb] ORCID: 0000-0003-3308-4549

Maintainer: Pierrick Roger <pierrick.roger at cea.fr>

Citation (from within R, enter citation("biodb")):

Pierrick Roger. biodb: Biodb, a Library and a Development Framework for Connecting to Chemical and Biological Databases. doi:10.18129/B9.bioc.biodb, R package version 1.20.0, https://bioconductor.org/packages/biodb.

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("biodb")

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("biodb")

Introduction to the biodb package.	HTML	R Script
Details on general biodb usage and principles	HTML	R Script
Manipulating entry objects	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Infrastructure, KEGG, Software
Version	1.20.0
In Bioconductor since	BioC 3.13 (R-4.1) (5.5 years)
License	AGPL-3
Depends	R (>= 4.1.0)
Imports	R6, RSQLite, Rcpp, XML, chk, fscache (>= 1.0.2), jsonlite, lgr, lifecycle, methods, openssl, plyr, progress, rappdirs, sched (>= 1.0.1), sqlq, stats, stringr, tools, withr, yaml
System Requirements
URL	https://gitlab.com/rbiodb/biodb
Bug Reports	https://gitlab.com/rbiodb/biodb/-/issues

Suggests	BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, xml2
Linking To	Rcpp, testthat
Enhances
Depends On Me
Imports Me	biodbChebi, phenomis
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	biodb_1.20.0.tar.gz
Windows Binary (x86_64)	biodb_1.20.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	biodb_1.20.0.tgz
macOS Binary (sonoma-arm64)	biodb_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/biodb
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/biodb
Package Short Url	https://bioconductor.org/packages/biodb/
Package Downloads Report	Download Stats