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>

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

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) (1.5 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
Package Short Url https://bioconductor.org/packages/biodb/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.16 Source Archive

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