biodb
This is thereleased version of biodb; for the devel version, seebiodb.
Biodb, a Library and a Development Framework for Connecting to Chemical and Biological Databases
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0001-8177-4873, Alexis Delabrière [ctb] ORCID: 0000-0003-3308-4549
Maintainer: Pierrick Roger <pierrick.roger at cea.fr>
citation("biodb")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("biodb")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("biodb")| 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 | 1.18.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (4.5 years) |
| License | AGPL-3 |
| Depends | R (>= 4.1.0) |
| Imports | R6,RSQLite,Rcpp,XML,chk,fscache (>= 1.0.2),jsonlite,lgr,lifecycle, methods,openssl,plyr,progress,rappdirs,sched (>= 1.0.1),sqlq, stats,stringr, tools,withr,yaml |
| System Requirements | |
| URL | https://gitlab.com/rbiodb/biodb |
| Bug Reports | https://gitlab.com/rbiodb/biodb/-/issues |
See More
| Suggests | BiocStyle,roxygen2,devtools,testthat (>= 2.0.0),knitr,rmarkdown,xml2 |
| Linking To | Rcpp,testthat |
| Enhances | |
| Depends On Me | |
| Imports Me | biodbChebi,phenomis |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | biodb_1.18.0.tar.gz |
| Windows Binary (x86_64) | biodb_1.18.0.zip |
| macOS Binary (x86_64) | biodb_1.18.0.tgz |
| macOS Binary (arm64) | biodb_1.18.0.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 |