OrganismDbi

DOI: 10.18129/B9.bioc.OrganismDbi  

Software to enable the smooth interfacing of different database packages

Bioconductor version: Release (3.17)

The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

Author: Marc Carlson [aut], Hervé Pagès [aut], Martin Morgan [aut], Valerie Obenchain [aut], Aliyu Atiku Mustapha [ctb] (Converted 'OrganismDbi' vignette from Sweave to RMarkdown / HTML.), Bioconductor Package Maintainer [cre]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("OrganismDbi")

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("OrganismDbi")

 

HTML	R Script	OrganismDbi: A meta framework for Annotation Packages
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Infrastructure, Software
Version	1.42.0
In Bioconductor since	BioC 2.11 (R-2.15) (11 years)
License	Artistic-2.0
Depends	R (>= 2.14.0), methods, BiocGenerics(>= 0.15.10), AnnotationDbi(>= 1.33.15), GenomicFeatures(>= 1.39.4)
Imports	Biobase, BiocManager, GenomicRanges(>= 1.31.13), graph, IRanges, RBGL, DBI, S4Vectors(>= 0.9.25), stats
LinkingTo
Suggests	Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me	Homo.sapiens, Mus.musculus, Rattus.norvegicus
Imports Me	AnnotationHubData, epivizrData, ggbio, uncoverappLib
Suggests Me	ChIPpeakAnno, epivizrStandalone
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	OrganismDbi_1.42.0.tar.gz
Windows Binary	OrganismDbi_1.42.0.zip (64-bit only)
macOS Binary (x86_64)	OrganismDbi_1.42.0.tgz
macOS Binary (arm64)	OrganismDbi_1.42.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/OrganismDbi
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/OrganismDbi
Bioc Package Browser	https://code.bioconductor.org/browse/OrganismDbi/
Package Short Url	https://bioconductor.org/packages/OrganismDbi/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive