All functions

GeneidFilter() GenebiotypeFilter() EntrezidFilter() TxidFilter() TxbiotypeFilter() ExonidFilter() ExonrankFilter() SeqnameFilter() SeqstrandFilter() SeqstartFilter() SeqendFilter()

Deprecated functionality

columns(<EnsDb>) keys(<EnsDb>) keytypes(<EnsDb>) mapIds(<EnsDb>) select(<EnsDb>)

Integration into the AnnotationDbi framework

dbconn(<EnsDb>) ensemblVersion(<EnsDb>) listColumns(<EnsDb>) listGenebiotypes(<EnsDb>) listTxbiotypes(<EnsDb>) listTables(<EnsDb>) metadata(<EnsDb>) organism(<EnsDb>) returnFilterColumns(<EnsDb>) returnFilterColumns(<EnsDb>) `returnFilterColumns<-`(<EnsDb>) seqinfo(<EnsDb>) seqlevels(<EnsDb>) updateEnsDb(<EnsDb>)

Basic usage of an Ensembl based annotation database

exons(<EnsDb>) exonsBy(<EnsDb>) intronsByTranscript(<EnsDb>) exonsByOverlaps(<EnsDb>) transcripts(<EnsDb>) transcriptsBy(<EnsDb>) transcriptsByOverlaps(<EnsDb>) promoters(<EnsDb>) genes(<EnsDb>) cdsBy(<EnsDb>) fiveUTRsByTranscript(<EnsDb>) threeUTRsByTranscript(<EnsDb>) toSAF(<GRangesList>)

Retrieve annotation data from an Ensembl based package

lengthOf(<EnsDb>)

Calculating lengths of features

seqlevelsStyle(<EnsDb>) `seqlevelsStyle<-`(<EnsDb>) supportedSeqlevelsStyles(<EnsDb>)

Support for other than Ensembl seqlevel style

getGenomeFaFile(<EnsDb>) getGenomeTwoBitFile(<EnsDb>)

Functionality related to DNA/RNA sequences

getGeneRegionTrackForGviz(<EnsDb>)

Utility functions

EnsDb()

Connect to an EnsDb object

OnlyCodingTxFilter() ProtDomIdFilter() ProteinDomainIdFilter() ProteinDomainSourceFilter() UniprotDbFilter() UniprotMappingTypeFilter() TxSupportLevelFilter() TxIsCanonicalFilter() TxExternalNameFilter() seqnames(<GRangesFilter>) seqlevels(<GRangesFilter>) supportedFilters(<EnsDb>)

Filters supported by ensembldb

proteins(<EnsDb>) listUniprotDbs(<EnsDb>) listUniprotMappingTypes(<EnsDb>) listProteinColumns()

Protein related functionality

cdsToTranscript()

Map positions within the CDS to coordinates relative to the start of the transcript

convertFilter(<AnnotationFilter>,<EnsDb>) convertFilter(<AnnotationFilterList>,<EnsDb>)

Convert an AnnotationFilter to a SQL WHERE condition for EnsDb

genomeToProtein()

Map genomic coordinates to protein coordinates

genomeToTranscript()

Map genomic coordinates to transcript coordinates

addFilter(<EnsDb>) dropFilter(<EnsDb>) activeFilter(<EnsDb>) filter()

Globally add filters to an EnsDb database

hasProteinData(<EnsDb>)

Determine whether protein data is available in the database

listEnsDbs()

List EnsDb databases in a MariaDB/MySQL server

ensDbFromAH() ensDbFromGRanges() ensDbFromGff() ensDbFromGtf() fetchTablesFromEnsembl() makeEnsemblSQLiteFromTables() makeEnsembldbPackage()

Generating a Ensembl annotation package from Ensembl

proteinToGenome(<EnsDb>)

Map within-protein coordinates to genomic coordinates

proteinToTranscript()

Map protein-relative coordinates to positions within the transcript

runEnsDbApp()

Search annotations interactively

transcriptToCds()

Map transcript-relative coordinates to positions within the CDS

transcriptToGenome()

Map transcript-relative coordinates to genomic coordinates

transcriptToProtein()

Map transcript-relative coordinates to amino acid residues of the encoded protein

useMySQL(<EnsDb>)

Use a MariaDB/MySQL backend