To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("ensembldb")

In most cases, you don't need to download the package archive at all.

ensembldb

Utilities to create and use an Ensembl based annotation database

Bioconductor version: 3.1

The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the ensembldb package provides also a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes.

Author: J. Rainer

Maintainer: Johannes Rainer <johannes.rainer at eurac.edu>

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

Installation

To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("ensembldb")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ensembldb")

 

PDF R Script Generating an using Ensembl based annotation packages
PDF   Reference Manual
Text   NEWS

Details

biocViews AnnotationData, Coverage, Genetics, Sequencing, Software
Version 1.0.1
In Bioconductor since BioC 3.1 (R-3.2) (< 6 months)
License LGPL
Depends BiocGenerics, GenomicRanges, GenomicFeatures
Imports methods, RSQLite, DBI, Biobase, GenomeInfoDb, AnnotationDbi, rtracklayer, S4Vectors
LinkingTo
Suggests knitr, BiocStyle, EnsDb.Hsapiens.v75(>= 0.99.7), RUnit
SystemRequirements
Enhances
URL
Depends On Me EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Mmusculus.v75, EnsDb.Mmusculus.v79, EnsDb.Rnorvegicus.v75, EnsDb.Rnorvegicus.v79
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source ensembldb_1.0.1.tar.gz
Windows Binary ensembldb_1.0.1.zip
Mac OS X 10.6 (Snow Leopard) ensembldb_1.0.1.tgz
Mac OS X 10.9 (Mavericks) ensembldb_1.0.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ensembldb/tree/release-3.1
Package Short Url http://bioconductor.org/packages/ensembldb/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center