biodb
This is the released version of biodb; for the devel version, see biodb.
Biodb, a Library and a Development Framework for Connecting to Chemical and Biological Databases
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| 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 | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (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 | |
| 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_1.20.0.tar.gz |
| Windows Binary (x86_64) | biodb_1.20.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | biodb_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | biodb_1.20.0.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 |