To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ensembldb")

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

ensembldb

   

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see ensembldb.

Utilities to create and use an Ensembl based annotation database

Bioconductor version: 3.4

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: Johannes Rainer <johannes.rainer at eurac.edu>, Tim Triche <tim.triche at usc.edu>

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:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ensembldb")

Documentation

HTML R Script Generating an using Ensembl based annotation packages
HTML R Script Using a MySQL server backend
PDF   Reference Manual
Text   NEWS

Details

biocViews AnnotationData, Coverage, Genetics, Sequencing, Software
Version 1.6.2
In Bioconductor since BioC 3.1 (R-3.2) (2 years)
License LGPL
Depends BiocGenerics(>= 0.15.10), GenomicRanges(>= 1.23.21), GenomicFeatures(>= 1.23.18)
Imports methods, RSQLite, DBI, Biobase, GenomeInfoDb, AnnotationDbi(>= 1.31.19), rtracklayer, S4Vectors, AnnotationHub, Rsamtools, IRanges
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, EnsDb.Hsapiens.v75(>= 0.99.7), RUnit, shiny, Gviz, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances RMySQL
URL https://github.com/jotsetung/ensembldb
BugReports https://github.com/jotsetung/ensembldb/issues
Depends On Me EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v75, EnsDb.Mmusculus.v79, EnsDb.Rnorvegicus.v75, EnsDb.Rnorvegicus.v79
Imports Me biovizBase, ChIPpeakAnno, ggbio, TVTB
Suggests Me alpine
Build Report  

Package Archives

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

Package Source ensembldb_1.6.2.tar.gz
Windows Binary ensembldb_1.6.2.zip
Mac OS X 10.9 (Mavericks) ensembldb_1.6.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ensembldb/tree/release-3.4
Package Short Url http://bioconductor.org/packages/ensembldb/
Package Downloads Report Download Stats

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