ensembldb

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see ensembldb.

Utilities to create and use Ensembl-based annotation databases

Bioconductor version: 3.6

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, the ensembldb package provides also a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes.

Author: Johannes Rainer <johannes.rainer at eurac.edu> with contributions from Tim Triche and Christian Weichenberger.

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

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

Installation

To install this package, start R (version "3.4") 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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AnnotationData, Coverage, Genetics, Sequencing, Software

Version 2.2.2

In Bioconductor since BioC 3.1 (R-3.2) (9 years)

License LGPL

Depends BiocGenerics(>= 0.15.10), GenomicRanges(>= 1.23.21), GenomicFeatures(>= 1.29.10), AnnotationFilter(>= 1.1.9)

Imports methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb, AnnotationDbi(>= 1.31.19), rtracklayer, S4Vectors, AnnotationHub, Rsamtools, IRanges(>= 2.11.16), ProtGenerics, Biostrings, curl

System Requirements

URL https://github.com/jotsetung/ensembldb

Bug Reports https://github.com/jotsetung/ensembldb/issues

Suggests BiocStyle, knitr, rmarkdown, EnsDb.Hsapiens.v75(>= 0.99.8), shiny, testthat, BSgenome.Hsapiens.UCSC.hg19, ggbio(>= 1.24.0), Gviz(>= 1.20.0), magrittr

Linking To

Enhances RMySQL

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, ChIPpeakAnno, epivizrData, ggbio, metagene, PathwaySplice, Pbase, TVTB

Suggests Me alpine, GenomicFeatures, wiggleplotr

Links To Me

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