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DOI: 10.18129/B9.bioc.ensembldb    

Utilities to create and use Ensembl-based annotation databases

Bioconductor version: Release (3.5)

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> with contributions from Tim Triche and Christian Weichenberger.

Maintainer: Johannes Rainer <johannes.rainer at>

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


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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


biocViews AnnotationData, Coverage, Genetics, Sequencing, Software
Version 2.0.4
In Bioconductor since BioC 3.1 (R-3.2) (2.5 years)
License LGPL
Depends BiocGenerics(>= 0.15.10), GenomicRanges(>= 1.23.21), GenomicFeatures(>= 1.23.18), AnnotationFilter(>= 0.99.7)
Imports methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb, AnnotationDbi(>= 1.31.19), rtracklayer, S4Vectors, AnnotationHub, Rsamtools, IRanges, ProtGenerics, Biostrings, curl
Suggests BiocStyle, knitr, rmarkdown, EnsDb.Hsapiens.v75(>= 0.99.8), shiny, testthat, BSgenome.Hsapiens.UCSC.hg19, ggbio(>= 1.24.0), Gviz(>= 1.20.0)
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, Pbase, TVTB
Suggests Me alpine, wiggleplotr
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