OrganismDbi

Software to enable the smooth interfacing of different database packages

Bioconductor version: Release (3.19)

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], 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>

Citation (from within R, enter citation("OrganismDbi")):

Installation

To install this package, start R (version "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Infrastructure, Software
Version	1.46.0
In Bioconductor since	BioC 2.11 (R-2.15) (12 years)
License	Artistic-2.0
Depends	R (>= 2.14.0), BiocGenerics(>= 0.15.10), AnnotationDbi(>= 1.33.15), GenomicFeatures(>= 1.39.4)
Imports	methods, utils, stats, DBI, BiocManager, Biobase, graph, RBGL, S4Vectors, IRanges, GenomicRanges(>= 1.31.13), txdbmaker
System Requirements
URL

Suggests	Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr
Linking To
Enhances
Depends On Me	Homo.sapiens, Mus.musculus, Rattus.norvegicus
Imports Me	AnnotationHubData, epivizrData, ggbio, uncoverappLib
Suggests Me	ChIPpeakAnno, epivizrStandalone
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	OrganismDbi_1.46.0.tar.gz
Windows Binary (x86_64)	OrganismDbi_1.46.0.zip
macOS Binary (x86_64)	OrganismDbi_1.46.0.tgz
macOS Binary (arm64)	OrganismDbi_1.46.0.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