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ensembldb

Utilities to create and use Ensembl-based annotation databases


Bioconductor version: Release (3.18)

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 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 "4.3") 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

Details

biocViews AnnotationData, Coverage, Genetics, Sequencing, Software
Version 2.26.0
In Bioconductor since BioC 3.1 (R-3.2) (9 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
See More
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 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 biovizBase, BUSpaRse, ChIPpeakAnno, consensusDE, diffUTR, drugTargetInteractions, epimutacions, epivizrData, GenomicDistributionsData, ggbio, GRaNIE, Gviz, metagene, proteasy, RAIDS, RITAN, scanMiRApp, scFeatures, scRNAseq, signifinder, singleCellTK, TVTB, tximeta
Suggests Me AnnotationHub, celldex, CNVRanger, eisaR, EpiTxDb, fishpond, GenomicFeatures, ldblock, multicrispr, nullranges, satuRn, wiggleplotr
Links To Me
Build Report Build Report

Package Archives

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

Source Package ensembldb_2.26.0.tar.gz
Windows Binary ensembldb_2.26.0.zip
macOS Binary (x86_64) ensembldb_2.26.0.tgz
macOS Binary (arm64) ensembldb_2.26.0.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