ensembldb
Utilities to create and use Ensembl-based annotation databases
Bioconductor version: 3.24 · Package version: 2.37.3
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ensembldb")Details
| Maintainer | Johannes Rainer <johannes.rainer@eurac.edu> |
| Author | Johannes Rainer <johannes.rainer@eurac.edu> with contributions from Tim Triche, Sebastian Gibb, Laurent Gatto Christian Weichenberger and Boyu Yu. |
| License | LGPL |
| URL | https://github.com/jorainer/ensembldb |
| Bug Reports | https://github.com/jorainer/ensembldb/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | AnnotationData, Coverage, Genetics, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/ensembldb/ |
Citation
From within R, enter citation("ensembldb"):
Johannes Rainer with contributions from Tim Triche, Sebastian Gibb, Laurent Gatto Christian Weichenberger and Boyu Yu. ensembldb: Utilities to create and use Ensembl-based annotation databases. doi:10.18129/B9.bioc.ensembldb, R package version 2.37.3, https://bioconductor.org/packages/ensembldb.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Generating and using Ensembl based annotation packages
- Mapping between genome, transcript and protein coordinates
- Querying protein features
- Use cases for coordinate mapping with ensembldb
- Using a MySQL server backend
Download
Follow the installation instructions to use this package in your R session.
| Source package | ensembldb_2.37.3.tar.gz |
| Windows binary (x86_64) | ensembldb_2.37.3.zip |
| macOS binary (arm64) | ensembldb_2.37.3.tgz |
| macOS binary (x86_64) | ensembldb_2.37.3.tgz |
Dependencies
Depends: R (>= 3.5.0), BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.61.1), GenomicFeatures (>= 1.61.4), AnnotationFilter (>= 1.5.2)
Imports: methods, RSQLite (>= 1.1), DBI, Biobase, Seqinfo, GenomeInfoDb (>= 1.45.5), AnnotationDbi (>= 1.31.19), rtracklayer (>= 1.69.1), S4Vectors (>= 0.23.10), Rsamtools, IRanges (>= 2.13.24), ProtGenerics, Biostrings (>= 2.77.2), curl
Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), rmarkdown, AnnotationHub
Reverse dependencies
Depends On Me (10): 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 (27): biovizBase, BUSpaRse, cellGeometry, chevreulProcess, ChIPpeakAnno, CleanUpRNAseq, damidBind, diffUTR, drugTargetInteractions, epivizrData, GenomicDistributionsData, ggbio, GPlinksR, GRaNIE, Gviz, locuszoomr, RAIDS, revert, RITAN, RNAseqQC, scanMiRApp, scFeatures, scRNAseq, signifinder, singleCellTK, TVTB, tximeta
Suggests Me (19): AlphaMissenseR, AnnotationHub, annotatr, autonomics, celldex, CNVRanger, eisaR, EpiTxDb, fishpond, gaawr2, GenomicFeatures, GRIN2, ldblock, multicrispr, nullranges, pQTLdata, satuRn, txdbmaker, wiggleplotr