ensembldb
Utilities to create and use Ensembl-based annotation databases
Bioconductor version: Release (3.17)
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("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 | ||
| NEWS | Text |
Details
| biocViews | AnnotationData, Coverage, Genetics, Sequencing, Software |
| Version | 2.24.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (8.5 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 |
| Linking To | |
| Suggests | BiocStyle, knitr, EnsDb.Hsapiens.v86(>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio(>= 1.24.0), Gviz(>= 1.20.0), rmarkdown, AnnotationHub |
| System Requirements | |
| Enhances | RMariaDB, shiny |
| URL | https://github.com/jorainer/ensembldb |
| Bug Reports | https://github.com/jorainer/ensembldb/issues |
See More
| 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, GRaNIE, Gviz, metagene, proteasy, RITAN, scanMiRApp, scFeatures, scRNAseq, signifinder, singleCellTK, TVTB, tximeta |
| Suggests Me | alpine, celldex, 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_2.24.0.tar.gz |
| Windows Binary | ensembldb_2.24.0.zip |
| macOS Binary (x86_64) | ensembldb_2.24.0.tgz |
| macOS Binary (arm64) | ensembldb_2.24.0.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 |