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biodb

This is the development version of biodb; for the stable release version, see biodb.

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

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
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 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, Infrastructure, KEGG, Software
Version 1.9.0
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
Linking To Rcpp, testthat
Suggests BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2, git2r
System Requirements
Enhances
URL https://github.com/pkrog/biodb
Bug Reports https://github.com/pkrog/biodb/issues
See More
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_1.9.0.tar.gz
Windows Binary biodb_1.9.0.zip
macOS Binary (x86_64) biodb_1.9.0.tgz
macOS Binary (arm64) biodb_1.9.0.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