ensembldb v1.2.0

by Johannes Rainer

Utilities to create and use an Ensembl based annotation database

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.

Functions in ensembldb

Name Description
GeneidFilter-class Filter results fetched from the Ensembl database
makeEnsembldbPackage Generating a Ensembl annotation package from Ensembl
EnsDb-class Basic usage of an Ensembl based annotation database
exonsBy Retrieve annotation data from an Ensembl based package
runEnsDbApp Search annotations interactively
SeqendFilter Constructor functions for filter objects
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Details

Type Package
URL https://github.com/jotsetung/ensembldb
BugReports https://github.com/jotsetung/ensembldb/issues
VignetteBuilder knitr
Collate Classes.R dbhelpers.R Methods.R Methods-Filter.R loadEnsDb.R makeEnsemblDbPackage.R EnsDbFromGTF.R runEnsDbApp.R zzz.R
biocViews Genetics, AnnotationData, Sequencing, Coverage
License LGPL

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