ensembldb: Utilities to create and use an Ensembl based annotation database

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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@eurac.edu>, Tim Triche <tim.triche@usc.edu>
Date of publication
None
Maintainer
Johannes Rainer <johannes.rainer@eurac.edu>
License
LGPL
Version
1.6.2
URLs

View on Bioconductor

Man pages

EnsDb
Connect to an EnsDb object
EnsDb-AnnotationDbi
Integration into the AnnotationDbi framework
EnsDb-class
Basic usage of an Ensembl based annotation database
EnsDb-exonsBy
Retrieve annotation data from an Ensembl based package
EnsDb-lengths
Calculating lengths of features
EnsDb-seqlevels
Support for other than Ensembl seqlevel style
EnsDb-sequences
Functionality related to DNA/RNA sequences
EnsDb-utils
Utility functions
GeneidFilter-class
Filter results fetched from the Ensembl database
listEnsDbs
List EnsDb databases in a MySQL server
makeEnsemblDbPackage
Generating a Ensembl annotation package from Ensembl
runEnsDbApp
Search annotations interactively
SeqendFilter
Constructor functions for filter objects
useMySQL-EnsDb-method
Use a MySQL backend

Files in this package

ensembldb/DESCRIPTION
ensembldb/NAMESPACE
ensembldb/R
ensembldb/R/Classes.R
ensembldb/R/EnsDbFromGTF.R
ensembldb/R/Generics.R
ensembldb/R/Methods-Filter.R
ensembldb/R/Methods.R
ensembldb/R/dbhelpers.R
ensembldb/R/functions-utils.R
ensembldb/R/loadEnsDb.R
ensembldb/R/makeEnsemblDbPackage.R
ensembldb/R/runEnsDbApp.R
ensembldb/R/select-methods.R
ensembldb/R/seqname-utils.R
ensembldb/R/zzz.R
ensembldb/build
ensembldb/build/vignette.rds
ensembldb/inst
ensembldb/inst/NEWS
ensembldb/inst/YGRanges.RData
ensembldb/inst/chrY
ensembldb/inst/chrY/ens_chromosome.txt
ensembldb/inst/chrY/ens_exon.txt
ensembldb/inst/chrY/ens_gene.txt
ensembldb/inst/chrY/ens_metadata.txt
ensembldb/inst/chrY/ens_tx.txt
ensembldb/inst/chrY/ens_tx2exon.txt
ensembldb/inst/doc
ensembldb/inst/doc/MySQL-backend.R
ensembldb/inst/doc/MySQL-backend.Rmd
ensembldb/inst/doc/MySQL-backend.html
ensembldb/inst/doc/ensembldb.R
ensembldb/inst/doc/ensembldb.Rmd
ensembldb/inst/doc/ensembldb.html
ensembldb/inst/perl
ensembldb/inst/perl/get_gene_transcript_exon_tables.pl
ensembldb/inst/pkg-template
ensembldb/inst/pkg-template/DESCRIPTION
ensembldb/inst/pkg-template/NAMESPACE
ensembldb/inst/pkg-template/R
ensembldb/inst/pkg-template/R/zzz.R
ensembldb/inst/pkg-template/man
ensembldb/inst/pkg-template/man/package.Rd
ensembldb/inst/shinyHappyPeople
ensembldb/inst/shinyHappyPeople/server.R
ensembldb/inst/shinyHappyPeople/ui.R
ensembldb/inst/test
ensembldb/inst/test/testFunctionality.R
ensembldb/inst/test/testInternals.R
ensembldb/inst/txt
ensembldb/inst/txt/ENST00000200135.fa.gz
ensembldb/inst/txt/ENST00000335953.fa.gz
ensembldb/inst/unitTests
ensembldb/inst/unitTests/test_Filters.R
ensembldb/inst/unitTests/test_Functionality.R
ensembldb/inst/unitTests/test_GFF.R
ensembldb/inst/unitTests/test_GRangeFilter.R
ensembldb/inst/unitTests/test_SymbolFilter.R
ensembldb/inst/unitTests/test_buildEdb.R
ensembldb/inst/unitTests/test_getGenomeFaFile.R
ensembldb/inst/unitTests/test_get_sequence.R
ensembldb/inst/unitTests/test_mysql.R
ensembldb/inst/unitTests/test_ordering.R
ensembldb/inst/unitTests/test_performance.R
ensembldb/inst/unitTests/test_returnCols.R
ensembldb/inst/unitTests/test_select.R
ensembldb/inst/unitTests/test_transcript_lengths.R
ensembldb/inst/unitTests/test_ucscChromosomeNames.R
ensembldb/inst/unitTests/test_validity.R
ensembldb/inst/unitTests/test_xByOverlap.R
ensembldb/man
ensembldb/man/EnsDb-AnnotationDbi.Rd
ensembldb/man/EnsDb-class.Rd
ensembldb/man/EnsDb-exonsBy.Rd
ensembldb/man/EnsDb-lengths.Rd
ensembldb/man/EnsDb-seqlevels.Rd
ensembldb/man/EnsDb-sequences.Rd
ensembldb/man/EnsDb-utils.Rd
ensembldb/man/EnsDb.Rd
ensembldb/man/GeneidFilter-class.Rd
ensembldb/man/SeqendFilter.Rd
ensembldb/man/listEnsDbs.Rd
ensembldb/man/makeEnsemblDbPackage.Rd
ensembldb/man/runEnsDbApp.Rd
ensembldb/man/useMySQL-EnsDb-method.Rd
ensembldb/tests
ensembldb/tests/runTests.R
ensembldb/vignettes
ensembldb/vignettes/MySQL-backend.Rmd
ensembldb/vignettes/MySQL-backend.org
ensembldb/vignettes/ensembldb.Rmd
ensembldb/vignettes/ensembldb.org
ensembldb/vignettes/images
ensembldb/vignettes/images/dblayout.png
ensembldb/vignettes/issues.org