# Utilities to create and use Ensembl-based annotation databases

## Documentation for package ‘ensembldb’ version 2.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G H K L M O P R S T U

## -- A --

activeFilter | Globally add filters to an EnsDb database
activeFilter-method | Globally add filters to an EnsDb database
addFilter | Globally add filters to an EnsDb database
addFilter-method | Globally add filters to an EnsDb database

## -- C --

cdsBy | Retrieve annotation data from an Ensembl based package
cdsBy-method | Retrieve annotation data from an Ensembl based package
cdsToTranscript | Map positions within the CDS to coordinates relative to the start of the transcript
columns-method | Integration into the AnnotationDbi framework
convertFilter-method | Convert an AnnotationFilter to a SQL WHERE condition for EnsDb

## -- D --

dbconn | Basic usage of an Ensembl based annotation database
dbconn-method | Basic usage of an Ensembl based annotation database
Deprecated | Deprecated functionality
disjointExons-method | Retrieve annotation data from an Ensembl based package
dropFilter | Globally add filters to an EnsDb database
dropFilter-method | Globally add filters to an EnsDb database

## -- E --

EnsDb | Connect to an EnsDb object
EnsDb-class | Basic usage of an Ensembl based annotation database
ensDbFromAH | Generating a Ensembl annotation package from Ensembl
ensDbFromGff | Generating a Ensembl annotation package from Ensembl
ensDbFromGRanges | Generating a Ensembl annotation package from Ensembl
ensDbFromGtf | Generating a Ensembl annotation package from Ensembl
ensembldb-deprecated | Deprecated functionality
ensemblVersion | Basic usage of an Ensembl based annotation database
ensemblVersion-method | Basic usage of an Ensembl based annotation database
EntrezidFilter | Deprecated functionality
ExonidFilter | Deprecated functionality
ExonrankFilter | Deprecated functionality
exons | Retrieve annotation data from an Ensembl based package
exons-method | Retrieve annotation data from an Ensembl based package
exonsBy | Retrieve annotation data from an Ensembl based package
exonsBy-method | Retrieve annotation data from an Ensembl based package
exonsByOverlaps-method | Retrieve annotation data from an Ensembl based package

## -- F --

fetchTablesFromEnsembl | Generating a Ensembl annotation package from Ensembl
filter | Globally add filters to an EnsDb database
Filter-classes | Filters supported by ensembldb
fiveUTRsByTranscript-method | Retrieve annotation data from an Ensembl based package

## -- G --

GenebiotypeFilter | Deprecated functionality
GeneidFilter | Deprecated functionality
genes | Retrieve annotation data from an Ensembl based package
genes-method | Retrieve annotation data from an Ensembl based package
genomeToProtein | Map genomic coordinates to protein coordinates
genomeToTranscript | Map genomic coordinates to transcript coordinates
getGeneRegionTrackForGviz | Utility functions
getGeneRegionTrackForGviz-method | Utility functions
getGenomeFaFile | Functionality related to DNA/RNA sequences
getGenomeFaFile-method | Functionality related to DNA/RNA sequences

## -- H --

hasProteinData | Determine whether protein data is available in the database
hasProteinData-method | Determine whether protein data is available in the database

## -- K --

keys-method | Integration into the AnnotationDbi framework
keytypes-method | Integration into the AnnotationDbi framework

## -- L --

lengthOf | Calculating lengths of features
lengthOf-method | Calculating lengths of features
listColumns | Basic usage of an Ensembl based annotation database
listColumns-method | Basic usage of an Ensembl based annotation database
listEnsDbs | List EnsDb databases in a MySQL server
listGenebiotypes | Basic usage of an Ensembl based annotation database
listGenebiotypes-method | Basic usage of an Ensembl based annotation database
listProteinColumns | Protein related functionality
listTables | Basic usage of an Ensembl based annotation database
listTables-method | Basic usage of an Ensembl based annotation database
listTxbiotypes | Basic usage of an Ensembl based annotation database
listTxbiotypes-method | Basic usage of an Ensembl based annotation database
listUniprotDbs | Protein related functionality
listUniprotDbs-method | Protein related functionality
listUniprotMappingTypes | Protein related functionality
listUniprotMappingTypes-method | Protein related functionality

## -- M --

makeEnsembldbPackage | Generating a Ensembl annotation package from Ensembl
makeEnsemblSQLiteFromTables | Generating a Ensembl annotation package from Ensembl
mapIds-method | Integration into the AnnotationDbi framework
metadata | Basic usage of an Ensembl based annotation database
metadata-method | Basic usage of an Ensembl based annotation database

## -- O --

OnlyCodingTxFilter | Filters supported by ensembldb
OnlyCodingTxFilter-class | Filters supported by ensembldb
organism | Basic usage of an Ensembl based annotation database
organism-method | Basic usage of an Ensembl based annotation database

## -- P --

promoters | Retrieve annotation data from an Ensembl based package
promoters-method | Retrieve annotation data from an Ensembl based package
ProtDomIdFilter | Filters supported by ensembldb
ProtDomIdFilter-class | Filters supported by ensembldb
ProteinDomainIdFilter | Filters supported by ensembldb
ProteinDomainIdFilter-class | Filters supported by ensembldb
ProteinDomainSourceFilter | Filters supported by ensembldb
ProteinDomainSourceFilter-class | Filters supported by ensembldb
proteins | Protein related functionality
proteins-method | Protein related functionality
proteinToGenome | Map within-protein coordinates to genomic coordinates
proteinToTranscript | Map protein-relative coordinates to positions within the transcript

## -- R --

returnFilterColumns | Basic usage of an Ensembl based annotation database
returnFilterColumns-method | Basic usage of an Ensembl based annotation database
returnFilterColumns<- | Basic usage of an Ensembl based annotation database
returnFilterColumns<--method | Basic usage of an Ensembl based annotation database
runEnsDbApp | Search annotations interactively

## -- S --

select | Integration into the AnnotationDbi framework
select-method | Integration into the AnnotationDbi framework
SeqendFilter | Deprecated functionality
seqinfo | Basic usage of an Ensembl based annotation database
seqinfo-method | Basic usage of an Ensembl based annotation database
seqlevels | Basic usage of an Ensembl based annotation database
seqlevels-method | Basic usage of an Ensembl based annotation database
seqlevels-method | Filters supported by ensembldb
seqlevelsStyle | Support for other than Ensembl seqlevel style
seqlevelsStyle-method | Support for other than Ensembl seqlevel style
seqlevelsStyle<- | Support for other than Ensembl seqlevel style
seqlevelsStyle<--method | Support for other than Ensembl seqlevel style
SeqnameFilter | Deprecated functionality
seqnames-method | Filters supported by ensembldb
SeqstartFilter | Deprecated functionality
SeqstrandFilter | Deprecated functionality
show | Basic usage of an Ensembl based annotation database
show-method | Basic usage of an Ensembl based annotation database
supportedFilters-method | Filters supported by ensembldb
supportedSeqlevelsStyles | Support for other than Ensembl seqlevel style
supportedSeqlevelsStyles-method | Support for other than Ensembl seqlevel style

## -- T --

threeUTRsByTranscript-method | Retrieve annotation data from an Ensembl based package
toSAF | Retrieve annotation data from an Ensembl based package
toSAF-method | Retrieve annotation data from an Ensembl based package
transcripts | Retrieve annotation data from an Ensembl based package
transcripts-method | Retrieve annotation data from an Ensembl based package
transcriptsBy | Retrieve annotation data from an Ensembl based package
transcriptsBy-method | Retrieve annotation data from an Ensembl based package
transcriptsByOverlaps-method | Retrieve annotation data from an Ensembl based package
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
TxbiotypeFilter | Deprecated functionality
TxidFilter | Deprecated functionality
TxSupportLevelFilter | Filters supported by ensembldb
TxSupportLevelFilter-class | Filters supported by ensembldb

## -- U --

UniprotDbFilter | Filters supported by ensembldb
UniprotDbFilter-class | Filters supported by ensembldb
UniprotMappingTypeFilter | Filters supported by ensembldb
UniprotMappingTypeFilter-class | Filters supported by ensembldb
updateEnsDb | Basic usage of an Ensembl based annotation database
updateEnsDb-method | Basic usage of an Ensembl based annotation database
useMySQL | Use a MySQL backend
useMySQL-method | Use a MySQL backend