ensembldb

DOI: 10.18129/B9.bioc.ensembldb  

Utilities to create and use Ensembl-based annotation databases

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	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
PDF		Reference Manual
Text		NEWS

Details

biocViews	AnnotationData, Coverage, Genetics, Sequencing, Software
Version	2.22.0
In Bioconductor since	BioC 3.1 (R-3.2) (8 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
LinkingTo
Suggests	BiocStyle, knitr, EnsDb.Hsapiens.v86(>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio(>= 1.24.0), Gviz(>= 1.20.0), magrittr, rmarkdown, AnnotationHub
SystemRequirements
Enhances	RMariaDB, shiny
URL	https://github.com/jorainer/ensembldb
BugReports	https://github.com/jorainer/ensembldb/issues
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, BUSpaRse, ChIPpeakAnno, consensusDE, diffUTR, drugTargetInteractions, epimutacions, epivizrData, GenomicDistributionsData, ggbio, Gviz, metagene, proteasy, RITAN, scanMiRApp, scRNAseq, signifinder, singleCellTK, TVTB, tximeta
Suggests Me	alpine, CNVRanger, dasper, eisaR, EpiTxDb, fishpond, GenomicFeatures, ldblock, multicrispr, nullranges, satuRn, wiggleplotr
Links To Me
Build Report

Package Archives

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

Source Package	ensembldb_2.22.0.tar.gz
Windows Binary	ensembldb_2.22.0.zip
macOS Binary (x86_64)	ensembldb_2.22.0.tgz
macOS Binary (arm64)	ensembldb_2.22.0.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