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OrganismDbi

This is the development version of OrganismDbi; for the stable release version, see OrganismDbi.

Software to enable the smooth interfacing of different database packages


Bioconductor version: Development (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], 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>

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Annotation, Infrastructure, Software
Version 1.45.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 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
System Requirements
URL
See More
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_1.45.0.tar.gz
Windows Binary OrganismDbi_1.45.0.zip
macOS Binary (x86_64) OrganismDbi_1.45.0.tgz
macOS Binary (arm64) OrganismDbi_1.45.0.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