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 (3.21)
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:
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")
# 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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, KEGG, Software |
| Version | 1.15.0 |
| 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, biodbHmdb, 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_1.15.0.tar.gz |
| Windows Binary (x86_64) | biodb_1.15.0.zip |
| macOS Binary (x86_64) | biodb_1.15.0.tgz |
| macOS Binary (arm64) | biodb_1.15.0.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 |