Package: ensembldb 2.37.3

Johannes Rainer

ensembldb: Utilities to create and use Ensembl-based annotation databases

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.

Authors:Johannes Rainer <[email protected]> with contributions from Tim Triche, Sebastian Gibb, Laurent Gatto Christian Weichenberger and Boyu Yu.

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ensembldb/json (API)

# Install 'ensembldb' in R:
install.packages('ensembldb', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jorainer/ensembldb/issues

On BioConductor:ensembldb-2.37.1(bioc 3.24)ensembldb-2.36.1(bioc 3.23)

geneticsannotationdatasequencingcoverageannotationbioconductorbioconductor-packagesensembl

13.40 score 36 stars 112 packages 1.7k scripts 18k downloads 90 exports 72 dependencies

Last updated from:eb82f264d2. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

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Exports:activeFilteraddFiltercdsBycdsToTranscriptcolumnsconvertFilterdbconndropFilterEnsDbensDbFromAHensDbFromGffensDbFromGRangesensDbFromGtfensemblVersionEntrezidFilterExonidFilterExonrankFilterexonsexonsByexonsByOverlapsfetchTablesFromEnsemblfilterfiveUTRsByTranscriptGenebiotypeFilterGeneidFiltergenesgenomeToProteingenomeToTranscriptgetGeneRegionTrackForGvizgetGenomeFaFilegetGenomeTwoBitFilehasProteinDataintronsByTranscriptkeyskeytypeslengthOflistColumnslistEnsDbslistGenebiotypeslistProteinColumnslistTableslistTxbiotypeslistUniprotDbslistUniprotMappingTypesmakeEnsembldbPackagemakeEnsemblSQLiteFromTablesmapIdsmetadataOnlyCodingTxFilterorganismpromotersProtDomIdFilterProteinDomainIdFilterProteinDomainSourceFilterproteinsproteinToGenomeproteinToTranscriptreturnFilterColumnsreturnFilterColumns<-runEnsDbAppselectSeqendFilterseqinfoseqlevelsseqlevelsStyleseqlevelsStyle<-SeqnameFilterseqnamesSeqstartFilterSeqstrandFiltershowsupportedFilterssupportedSeqlevelsStylesthreeUTRsByTranscripttoSAFtranscriptstranscriptsBytranscriptsByOverlapstranscriptToCdstranscriptToGenometranscriptToProteinTxbiotypeFilterTxExternalNameFilterTxidFilterTxIsCanonicalFilterTxSupportLevelFilterUniprotDbFilterUniprotMappingTypeFilterupdateEnsDbuseMySQL

Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelazyevallifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngProtGenericsR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryaml

Generating and using Ensembl based annotation packages
Introduction | Using ensembldb annotation packages to retrieve specific annotations | Extracting gene/transcript/exon models for RNASeq feature counting | Retrieving sequences for gene/transcript/exon models | Integrating annotations from Ensembl based EnsDb packages with UCSC based annotations | Interactive annotation lookup using the shiny web app | Plotting gene/transcript features using ensembldb and Gviz and ggbio | Using EnsDb objects in the AnnotationDbi framework | Important notes | Getting or building EnsDb databases/packages | Getting EnsDb databases | Building annotation packages | Database layout<a id="org4707794"></a> | Session information | Footnotes
Rendered fromensembldb.Rmdusingknitr::rmarkdown

Last update: 2025-08-18
Started: 2018-02-28

Querying protein features
Introduction | Fetch protein annotation for genes and transcripts | Use methods from the AnnotationDbi package to query protein annotation | Retrieve proteins from the database | Map peptide features within proteins to the genome | Session information
Rendered fromproteins.Rmdusingknitr::rmarkdown

Last update: 2024-08-21
Started: 2018-02-28

Using a MySQL server backend
Introduction | Using ensembldb with a MySQL server | Session information
Rendered fromMySQL-backend.Rmdusingknitr::rmarkdown

Last update: 2024-08-21
Started: 2018-02-28

Use cases for coordinate mapping with ensembldb
Query for helix-loop-helix transcription factors on chromosome 21 | Mapping of genomic coordinates to protein-relative positions | Session information | References
Rendered fromcoordinate-mapping-use-cases.Rmdusingknitr::rmarkdown

Last update: 2022-01-31
Started: 2018-11-13

Mapping between genome, transcript and protein coordinates
Introduction | Mapping genomic coordinates to transcript-relative coordinates | Mapping genomic coordinates to protein-relative coordinates | Mapping protein coordinates to transcript coordinates | Mapping protein coordinates to the genome | Mapping transcript coordinates to genomic coordinates | Mapping transcript coordinates to protein coordinates | Session information
Rendered fromcoordinate-mapping.Rmdusingknitr::rmarkdown

Last update: 2020-01-22
Started: 2018-02-28

Readme and manuals

Help Manual

Help pageTopics
Globally add filters to an EnsDb databaseactiveFilter activeFilter,EnsDb-method addFilter addFilter,EnsDb-method dropFilter dropFilter,EnsDb-method filter
Map positions within the CDS to coordinates relative to the start of the transcriptcdsToTranscript
Convert an AnnotationFilter to a SQL WHERE condition for EnsDbconvertFilter,AnnotationFilter,EnsDb-method convertFilter,AnnotationFilterList,EnsDb-method
Deprecated functionalityDeprecated ensembldb-deprecated EntrezidFilter ExonidFilter ExonrankFilter GenebiotypeFilter GeneidFilter SeqendFilter SeqnameFilter SeqstartFilter SeqstrandFilter TxbiotypeFilter TxidFilter
Connect to an EnsDb objectEnsDb
Basic usage of an Ensembl based annotation databasedbconn dbconn,EnsDb-method EnsDb-class ensemblVersion ensemblVersion,EnsDb-method genome<-,EnsDb-method listColumns listColumns,EnsDb-method listGenebiotypes listGenebiotypes,EnsDb-method listTables listTables,EnsDb-method listTxbiotypes listTxbiotypes,EnsDb-method metadata metadata,EnsDb-method organism organism,EnsDb-method returnFilterColumns returnFilterColumns,EnsDb-method returnFilterColumns<- returnFilterColumns<-,EnsDb-method seqinfo seqinfo,EnsDb-method seqlevels seqlevels,EnsDb-method show show,EnsDb-method updateEnsDb updateEnsDb,EnsDb-method
Retrieve annotation data from an Ensembl based packagecdsBy cdsBy,EnsDb-method exons exons,EnsDb-method exonsBy exonsBy,EnsDb-method exonsByOverlaps,EnsDb-method fiveUTRsByTranscript,EnsDb-method genes genes,EnsDb-method intronsByTranscript,EnsDb-method promoters promoters,EnsDb-method threeUTRsByTranscript,EnsDb-method toSAF toSAF,GRangesList-method transcripts transcripts,EnsDb-method transcriptsBy transcriptsBy,EnsDb-method transcriptsByOverlaps,EnsDb-method
Filters supported by ensembldbFilter-classes OnlyCodingTxFilter OnlyCodingTxFilter-class ProtDomIdFilter ProtDomIdFilter-class ProteinDomainIdFilter ProteinDomainIdFilter-class ProteinDomainSourceFilter ProteinDomainSourceFilter-class seqlevels,GRangesFilter-method seqnames,GRangesFilter-method supportedFilters,EnsDb-method TxExternalNameFilter TxExternalNameFilter-class TxIsCanonicalFilter TxIsCanonicalFilter-class TxSupportLevelFilter TxSupportLevelFilter-class UniprotDbFilter UniprotDbFilter-class UniprotMappingTypeFilter UniprotMappingTypeFilter-class
Map genomic coordinates to protein coordinatesgenomeToProtein
Map genomic coordinates to transcript coordinatesgenomeToTranscript
Utility functionsgetGeneRegionTrackForGviz getGeneRegionTrackForGviz,EnsDb-method
Functionality related to DNA/RNA sequencesgetGenomeFaFile getGenomeFaFile,EnsDb-method getGenomeTwoBitFile getGenomeTwoBitFile,EnsDb-method
Determine whether protein data is available in the databasehasProteinData hasProteinData,EnsDb-method
Calculating lengths of featureslengthOf lengthOf,EnsDb-method lengthOf,GRangesList-method
List EnsDb databases in a MariaDB/MySQL serverlistEnsDbs
Generating a Ensembl annotation package from EnsemblensDbFromAH ensDbFromGff ensDbFromGRanges ensDbFromGtf fetchTablesFromEnsembl makeEnsembldbPackage makeEnsemblSQLiteFromTables
Protein related functionalitylistProteinColumns listUniprotDbs listUniprotDbs,EnsDb-method listUniprotMappingTypes listUniprotMappingTypes,EnsDb-method proteins proteins,EnsDb-method
Map within-protein coordinates to genomic coordinatesproteinToGenome proteinToGenome,CompressedGRangesList-method proteinToGenome,EnsDb-method proteinToGenome,Preloaded-method
Map protein-relative coordinates to positions within the transcriptproteinToTranscript proteinToTranscript,CompressedGRangesList-method proteinToTranscript,EnsDb-method proteinToTranscript,Preloaded-method
Search annotations interactivelyrunEnsDbApp
Integration into the AnnotationDbi frameworkcolumns,EnsDb-method keys,EnsDb-method keytypes,EnsDb-method mapIds,EnsDb-method select select,EnsDb-method
Support for other than Ensembl seqlevel styleseqlevelsStyle seqlevelsStyle,EnsDb-method seqlevelsStyle<- seqlevelsStyle<-,EnsDb-method supportedSeqlevelsStyles supportedSeqlevelsStyles,EnsDb-method
Map transcript-relative coordinates to positions within the CDStranscriptToCds
Map transcript-relative coordinates to genomic coordinatestranscriptToGenome
Map transcript-relative coordinates to amino acid residues of the encoded proteintranscriptToProtein
Use a MariaDB/MySQL backenduseMySQL useMySQL,EnsDb-method