ensembldb: 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.

AuthorJohannes Rainer <johannes.rainer@eurac.edu>, Tim Triche <tim.triche@usc.edu>
Date of publicationNone
MaintainerJohannes Rainer <johannes.rainer@eurac.edu>
LicenseLGPL
Version1.6.2
https://github.com/jotsetung/ensembldb

View on Bioconductor

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

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