To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("ensembldb")

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

ensembldb

DOI: 10.18129/B9.bioc.ensembldb    

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

Utilities to create and use Ensembl-based annotation databases

Bioconductor version: Development (3.7)

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, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.

Author: Johannes Rainer <johannes.rainer at eurac.edu> with contributions from Tim Triche, Sebastian Gibb, Laurent Gatto and Christian Weichenberger.

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("http://bioc.ism.ac.jp/biocLite.R")
biocLite("ensembldb")

Documentation

HTML R Script Generating an using Ensembl based annotation packages
HTML R Script Mapping between genome, transcript and protein coordinates
HTML R Script Querying protein features
HTML R Script Using a MySQL server backend
PDF   Reference Manual
Text   NEWS

Details

biocViews AnnotationData, Coverage, Genetics, Sequencing, Software
Version 2.3.5
In Bioconductor since BioC 3.1 (R-3.2) (2.5 years)
License LGPL
Depends BiocGenerics(>= 0.15.10), GenomicRanges(>= 1.23.21), GenomicFeatures(>= 1.29.10), AnnotationFilter(>= 1.1.9)
Imports methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb, AnnotationDbi(>= 1.31.19), rtracklayer, S4Vectors, Rsamtools, IRanges(>= 2.11.16), ProtGenerics, Biostrings, curl
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, EnsDb.Hsapiens.v75(>= 0.99.8), testthat, BSgenome.Hsapiens.UCSC.hg19, ggbio(>= 1.24.0), Gviz(>= 1.20.0), magrittr, AnnotationHub
SystemRequirements
Enhances RMySQL, shiny
URL https://github.com/jotsetung/ensembldb
BugReports https://github.com/jotsetung/ensembldb/issues
Depends On Me AHEnsDbs, chimeraviz, 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, epivizrData, ggbio, metagene, PathwaySplice, Pbase, TVTB
Suggests Me alpine, GenomicFeatures, wiggleplotr
Build Report  

Package Archives

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

Source Package ensembldb_2.3.5.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) ensembldb_2.3.5.tgz
Source Repository git clone https://git.bioconductor.org/packages/ensembldb
Package Short Url http://bioconductor.org/packages/ensembldb/
Package Downloads Report Download Stats

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