ensembldb

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see ensembldb.

Utilities to create and use Ensembl-based annotation databases

Bioconductor version: 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>

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

Installation

To install this package, start R (version "3.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ensembldb")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AnnotationData, Coverage, Genetics, Sequencing, Software
Version	2.2.2
In Bioconductor since	BioC 3.1 (R-3.2) (9 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
System Requirements
URL	https://github.com/jotsetung/ensembldb
Bug Reports	https://github.com/jotsetung/ensembldb/issues

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
Linking To
Enhances	RMySQL
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
Links To Me
Build Report	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
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ensembldb
Package Short Url	https://bioconductor.org/packages/ensembldb/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive