OrganismDbi

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see OrganismDbi.

Software to enable the smooth interfacing of different database packages

Bioconductor version: 3.21

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 "4.5") 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 1.50.0

In Bioconductor since BioC 2.11 (R-2.15) (13 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_1.50.0.tar.gz

Windows Binary (x86_64) OrganismDbi_1.50.0.zip (64-bit only)

macOS Binary (x86_64) OrganismDbi_1.50.0.tgz

macOS Binary (arm64) OrganismDbi_1.50.0.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/

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