# Utilities to create and use an Ensembl based annotation database

## Documentation for package ‘ensembldb’ version 1.6.2

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

## Help Pages

B C D E F G K L M O P R S T U V W

## -- B --

BasicFilter-class | Filter results fetched from the Ensembl database
buildQuery | Basic usage of an Ensembl based annotation database
buildQuery-method | Basic usage of an Ensembl based annotation database

## -- C --

cdsBy | Retrieve annotation data from an Ensembl based package
cdsBy-method | Retrieve annotation data from an Ensembl based package
column | Filter results fetched from the Ensembl database
column-method | Filter results fetched from the Ensembl database
columns-method | Integration into the AnnotationDbi framework
condition | Filter results fetched from the Ensembl database
condition-method | Filter results fetched from the Ensembl database
condition<- | Filter results fetched from the Ensembl database
condition<--method | Filter results fetched from the Ensembl database

## -- D --

dbconn | Basic usage of an Ensembl based annotation database
dbconn-method | Basic usage of an Ensembl based annotation database
disjointExons-method | Retrieve annotation data from an Ensembl based package

## -- E --

end-method | Filter results fetched from the Ensembl database
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
ensemblVersion | Basic usage of an Ensembl based annotation database
ensemblVersion-method | Basic usage of an Ensembl based annotation database
EntrezidFilter | Constructor functions for filter objects
EntrezidFilter-class | Filter results fetched from the Ensembl database
ExonidFilter | Constructor functions for filter objects
ExonidFilter-class | Filter results fetched from the Ensembl database
ExonrankFilter | Constructor functions for filter objects
ExonrankFilter-class | Filter results fetched from the Ensembl database
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
fiveUTRsByTranscript-method | Retrieve annotation data from an Ensembl based package

## -- G --

GenebiotypeFilter | Constructor functions for filter objects
GenebiotypeFilter-class | Filter results fetched from the Ensembl database
GeneidFilter | Constructor functions for filter objects
GeneidFilter-class | Filter results fetched from the Ensembl database
GenenameFilter | Constructor functions for filter objects
GenenameFilter-class | Filter results fetched from the Ensembl database
genes | Retrieve annotation data from an Ensembl based package
genes-method | Retrieve annotation data from an Ensembl based package
getGeneRegionTrackForGviz | Utility functions
getGeneRegionTrackForGviz-method | Utility functions
getGenomeFaFile | Functionality related to DNA/RNA sequences
getGenomeFaFile-method | Functionality related to DNA/RNA sequences
GRangesFilter | Constructor functions for filter objects
GRangesFilter-class | Filter results fetched from the Ensembl 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
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

## -- 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 --

organism | Basic usage of an Ensembl based annotation database
organism-method | Basic usage of an Ensembl based annotation database

## -- P --

print-method | Filter results fetched from the Ensembl database
promoters | Retrieve annotation data from an Ensembl based package
promoters-method | Retrieve annotation data from an Ensembl based package

## -- 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 | Constructor functions for filter objects
SeqendFilter-class | Filter results fetched from the Ensembl database
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 | Filter results fetched from the Ensembl database
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 | Constructor functions for filter objects
SeqnameFilter-class | Filter results fetched from the Ensembl database
seqnames-method | Filter results fetched from the Ensembl database
SeqstartFilter | Constructor functions for filter objects
SeqstartFilter-class | Filter results fetched from the Ensembl database
SeqstrandFilter | Constructor functions for filter objects
SeqstrandFilter-class | Filter results fetched from the Ensembl database
show | Basic usage of an Ensembl based annotation database
show-method | Basic usage of an Ensembl based annotation database
show-method | Filter results fetched from the Ensembl database
start-method | Filter results fetched from the Ensembl database
strand-method | Filter results fetched from the Ensembl database
supportedSeqlevelsStyles | Support for other than Ensembl seqlevel style
supportedSeqlevelsStyles-method | Support for other than Ensembl seqlevel style
SymbolFilter | Constructor functions for filter objects
SymbolFilter-class | Filter results fetched from the Ensembl database

## -- 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
TxbiotypeFilter | Constructor functions for filter objects
TxbiotypeFilter-class | Filter results fetched from the Ensembl database
TxidFilter | Constructor functions for filter objects
TxidFilter-class | Filter results fetched from the Ensembl database

## -- U --

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

## -- V --

value | Filter results fetched from the Ensembl database
value-method | Filter results fetched from the Ensembl database
value<- | Filter results fetched from the Ensembl database
value<--method | Filter results fetched from the Ensembl database

## -- W --

where | Filter results fetched from the Ensembl database
where-method | Filter results fetched from the Ensembl database