ensembldb

DOI: 10.18129/B9.bioc.ensembldb    

Utilities to create and use Ensembl-based annotation databases

Bioconductor version: Release (3.6)

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> with contributions from Tim Triche and Christian Weichenberger.

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

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	Querying protein features
HTML	R Script	Using a MySQL server backend
PDF		Reference Manual
Text		NEWS

Details

biocViews	AnnotationData, Coverage, Genetics, Sequencing, Software
Version	2.2.2
In Bioconductor since	BioC 3.1 (R-3.2) (3 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, AnnotationHub, Rsamtools, IRanges(>= 2.11.16), ProtGenerics, Biostrings, curl
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, EnsDb.Hsapiens.v75(>= 0.99.8), shiny, testthat, BSgenome.Hsapiens.UCSC.hg19, ggbio(>= 1.24.0), Gviz(>= 1.20.0), magrittr
SystemRequirements
Enhances	RMySQL
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_2.2.2.tar.gz
Windows Binary	ensembldb_2.2.2.zip
Mac OS X 10.11 (El Capitan)	ensembldb_2.2.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ensembldb
Package Short Url	http://bioconductor.org/packages/ensembldb/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive