biodb

DOI: 10.18129/B9.bioc.biodb  

biodb, a library and a development framework for connecting to chemical and biological databases

Bioconductor version: Release (3.16)

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] , Alexis Delabrière [ctb]

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

Installation

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

 

HTML	R Script	Creating a new connector class for accessing a database.
HTML	R Script	Creating a new field for entries.
HTML	R Script	Details on general *biodb* usage and principles
HTML	R Script	Introduction to the biodb package.
HTML	R Script	Manipulating entry objects
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, Infrastructure, KEGG, Software
Version	1.6.1
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	AGPL-3
Depends	R (>= 4.1.0)
Imports	BiocFileCache, R6, RCurl, RSQLite, Rcpp, XML, chk, jsonlite, lgr, lifecycle, methods, openssl, plyr, progress, rappdirs, stats, stringr, tools, withr, yaml
LinkingTo	Rcpp, testthat
Suggests	BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2, git2r
SystemRequirements
Enhances
URL	https://github.com/pkrog/biodb
BugReports	https://github.com/pkrog/biodb/issues
Depends On Me
Imports Me	biodbChebi, biodbExpasy, biodbHmdb, biodbKegg, biodbLipidmaps, biodbMirbase, biodbNcbi, biodbNci, biodbUniprot, phenomis
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	biodb_1.6.1.tar.gz
Windows Binary	biodb_1.6.1.zip (64-bit only)
macOS Binary (x86_64)	biodb_1.6.1.tgz
macOS Binary (arm64)	biodb_1.6.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/biodb
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/biodb
Bioc Package Browser	https://code.bioconductor.org/browse/biodb/
Package Short Url	https://bioconductor.org/packages/biodb/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive