ensembldb

Utilities to create and use Ensembl-based annotation databases

Bioconductor version: Release (3.20)

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 Christian Weichenberger and Boyu Yu.

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

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

Installation

To install this package, start R (version "4.4") 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

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

browseVignettes("ensembldb")

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
Use cases for coordinate mapping with ensembldb	HTML	R Script
Using a MariaDB/MySQL server backend	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AnnotationData, Coverage, Genetics, Sequencing, Software
Version	2.30.0
In Bioconductor since	BioC 3.1 (R-3.2) (9.5 years)
License	LGPL
Depends	R (>= 3.5.0), BiocGenerics(>= 0.15.10), GenomicRanges(>= 1.31.18), GenomicFeatures(>= 1.49.6), AnnotationFilter(>= 1.5.2)
Imports	methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb, AnnotationDbi(>= 1.31.19), rtracklayer, S4Vectors(>= 0.23.10), Rsamtools, IRanges(>= 2.13.24), ProtGenerics, Biostrings(>= 2.47.9), curl
System Requirements
URL	https://github.com/jorainer/ensembldb
Bug Reports	https://github.com/jorainer/ensembldb/issues

Suggests	BiocStyle, knitr, EnsDb.Hsapiens.v86(>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio(>= 1.24.0), Gviz(>= 1.20.0), rmarkdown, AnnotationHub
Linking To
Enhances	RMariaDB, shiny
Depends On Me	chimeraviz, demuxSNP, AHEnsDbs, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v75, EnsDb.Mmusculus.v79, EnsDb.Rnorvegicus.v75, EnsDb.Rnorvegicus.v79
Imports Me	biovizBase, BUSpaRse, ChIPpeakAnno, CleanUpRNAseq, consensusDE, diffUTR, epimutacions, epivizrData, ggbio, GRaNIE, Gviz, RAIDS, RITAN, scanMiRApp, scFeatures, singleCellTK, TVTB, tximeta, GenomicDistributionsData, scRNAseq, crosstalkr, locuszoomr, MOCHA, RNAseqQC
Suggests Me	AlphaMissenseR, AnnotationHub, autonomics, CNVRanger, eisaR, EpiTxDb, fishpond, GenomicFeatures, ldblock, multicrispr, nullranges, satuRn, txdbmaker, wiggleplotr, celldex, GeneSelectR
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	ensembldb_2.30.0.tar.gz
Windows Binary (x86_64)	ensembldb_2.30.0.zip
macOS Binary (x86_64)	ensembldb_2.30.0.tgz
macOS Binary (arm64)	ensembldb_2.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ensembldb
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ensembldb
Bioc Package Browser	https://code.bioconductor.org/browse/ensembldb/
Package Short Url	https://bioconductor.org/packages/ensembldb/
Package Downloads Report	Download Stats