ensembldb
This is the released version of ensembldb; for the devel version, see ensembldb.
All Bioconductor versions of ensembldb
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1
Utilities to create and use Ensembl-based annotation databases
Bioconductor version: 3.23 · Package version: 2.36.1
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"):
Johannes Rainer with contributions from Tim Triche, Sebastian Gibb, Laurent Gatto Christian Weichenberger and Boyu Yu. ensembldb: Utilities to create and use Ensembl-based annotation databases. doi:10.18129/B9.bioc.ensembldb, R package version 2.36.1, https://bioconductor.org/packages/ensembldb.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 2.36.1 |
| License | LGPL |
| URL | https://github.com/jorainer/ensembldb |
| Bug Reports | https://github.com/jorainer/ensembldb/issues |
| Last updated | 2026-05-25 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11 years) |
| Downloads rank | 72 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | AnnotationData, Coverage, Genetics, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/ensembldb/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ensembldb")| Generating and 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 MySQL server backend | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | ensembldb_2.36.1.tar.gz |
| Windows binary (x86_64) | ensembldb_2.36.1.zip |
| macOS binary (arm64) | ensembldb_2.36.1.tgz |
| macOS binary (x86_64) | ensembldb_2.36.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ensembldb |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ensembldb |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |
Dependencies
Depends: R (>= 3.5.0), BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.61.1), GenomicFeatures (>= 1.61.4), AnnotationFilter (>= 1.5.2)
Imports: methods, RSQLite (>= 1.1), DBI, Biobase, Seqinfo, GenomeInfoDb (>= 1.45.5), AnnotationDbi (>= 1.31.19), rtracklayer (>= 1.69.1), S4Vectors (>= 0.23.10), Rsamtools, IRanges (>= 2.13.24), ProtGenerics, Biostrings (>= 2.77.2), curl
Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), rmarkdown, AnnotationHub
Reverse dependencies
Depends On Me (10): AHEnsDbs, chimeraviz, demuxSNP, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v75, EnsDb.Mmusculus.v79, EnsDb.Rnorvegicus.v75, EnsDb.Rnorvegicus.v79
Imports Me (27): biovizBase, BUSpaRse, cellGeometry, chevreulProcess, ChIPpeakAnno, CleanUpRNAseq, damidBind, diffUTR, drugTargetInteractions, epimutacions, epivizrData, GenomicDistributionsData, ggbio, GRaNIE, Gviz, locuszoomr, RAIDS, revert, RITAN, RNAseqQC, scanMiRApp, scFeatures, scRNAseq, signifinder, singleCellTK, TVTB, tximeta
Suggests Me (18): AlphaMissenseR, AnnotationHub, autonomics, celldex, CNVRanger, eisaR, EpiTxDb, fishpond, gaawr2, GenomicFeatures, GRIN2, ldblock, multicrispr, nullranges, pQTLdata, satuRn, txdbmaker, wiggleplotr