biodb
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see biodb.
biodb, a library and a development framework for connecting to chemical and biological databases
Bioconductor version: 3.13
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 "4.1") 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 |
| In-house compound database | HTML | R Script |
| In-house LCMS database | 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 | 1.0.4 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 years) |
| License | AGPL-3 |
| Depends | R (>= 4.0) |
| Imports | R6, methods, chk, lgr, progress, lifecycle, XML, stringr, plyr, yaml, jsonlite, RCurl, Rcpp, rappdirs, stats, openssl, RSQLite, withr |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2, git2r |
| Linking To | Rcpp, testthat |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| 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_1.0.4.tar.gz |
| Windows Binary | biodb_1.0.4.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | biodb_1.0.4.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 |
| Old Source Packages for BioC 3.13 | Source Archive |