biodb
biodb, a library and a development framework for connecting to chemical and biological databases
Bioconductor version: Release (3.19)
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("biodb")
):
Installation
To install this package, start R (version "4.4") 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")
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 | ||
NEWS | Text |
Details
biocViews | DataImport, Infrastructure, KEGG, Software |
Version | 1.12.0 |
In Bioconductor since | BioC 3.13 (R-4.1) (3.5 years) |
License | AGPL-3 |
Depends | R (>= 4.1.0) |
Imports | BiocFileCache, R6, RCurl, RSQLite, Rcpp, XML, chk, git2r, jsonlite, lgr, lifecycle, methods, openssl, plyr, progress, rappdirs, stats, stringr, tools, withr, yaml |
System Requirements | |
URL | https://github.com/pkrog/biodb |
Bug Reports | https://github.com/pkrog/biodb/issues |
See More
Suggests | BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2 |
Linking To | Rcpp, testthat |
Enhances | |
Depends On Me | |
Imports Me | biodbChebi, biodbExpasy, biodbHmdb, biodbKegg, biodbLipidmaps, biodbNcbi, biodbNci, biodbUniprot, phenomis |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | biodb_1.12.0.tar.gz |
Windows Binary | biodb_1.12.0.zip |
macOS Binary (x86_64) | biodb_1.12.0.tgz |
macOS Binary (arm64) | biodb_1.12.0.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 |