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Bioconductor - ensembldb (development version)

ensembldb

This is the development version of ensembldb; for the stable release version, see ensembldb.

Utilities to create and use Ensembl-based annotation databases

Bioconductor version: Development (3.22)

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 Christian Weichenberger and Boyu Yu.

Maintainer: Johannes Rainer <johannes.rainer at eurac.edu>

Citation (from within R, enter citation("ensembldb")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

Details biocViews AnnotationData, Coverage, Genetics, Sequencing, Software Version 2.33.1 In Bioconductor since BioC 3.1 (R-3.2) (10 years) License LGPL 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 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 chimeraviz, demuxSNP, AHEnsDbs, 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, chevreulProcess, ChIPpeakAnno, CleanUpRNAseq, consensusDE, diffUTR, epimutacions, epivizrData, ggbio, GRaNIE, Gviz, RAIDS, RITAN, scanMiRApp, scFeatures, signifinder, TVTB, tximeta, GenomicDistributionsData, scRNAseq, crosstalkr, locuszoomr, RNAseqQC Suggests Me AlphaMissenseR, AnnotationHub, autonomics, CNVRanger, eisaR, EpiTxDb, fishpond, GenomicFeatures, ldblock, multicrispr, nullranges, satuRn, txdbmaker, wiggleplotr, celldex, gaawr2, GeneSelectR, GRIN2, pQTLdata Links To Me Build Report Build Report Package Archives

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

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