DOI: 10.18129/B9.bioc.ensembldb    

Utilities to create and use Ensembl-based annotation databases

Bioconductor version: Release (3.14)

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")):


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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


biocViews AnnotationData, Coverage, Genetics, Sequencing, Software
Version 2.18.2
In Bioconductor since BioC 3.1 (R-3.2) (6.5 years)
License LGPL
Depends BiocGenerics(>= 0.15.10), GenomicRanges(>= 1.31.18), GenomicFeatures(>= 1.29.10), 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
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
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 APAlyzer, biovizBase, BUSpaRse, ChIPpeakAnno, consensusDE, diffUTR, drugTargetInteractions, epivizrData, GenomicDistributionsData, ggbio, Gviz, ldblock, metagene, scanMiRApp, scRNAseq, TVTB, tximeta
Suggests Me alpine, CNVRanger, dasper, eisaR, EpiTxDb, GenomicFeatures, multicrispr, satuRn, wiggleplotr
Links To Me
Build Report  

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Source Package ensembldb_2.18.2.tar.gz
Windows Binary ensembldb_2.18.2.zip
macOS 10.13 (High Sierra) ensembldb_2.18.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/ensembldb
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ensembldb
Package Short Url https://bioconductor.org/packages/ensembldb/
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