biodb

DOI: 10.18129/B9.bioc.biodb    

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

Bioconductor version: Release (3.14)

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 "4.1") 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	1.2.2
In Bioconductor since	BioC 3.13 (R-4.1) (1 year)
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, biodbHmdb, biodbKegg, biodbLipidmaps, biodbUniprot
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	biodb_1.2.2.tar.gz
Windows Binary	biodb_1.2.2.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	biodb_1.2.2.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
Old Source Packages for BioC 3.14	Source Archive