Utilities to create and use an Ensembl based annotation database


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Documentation for package ‘ensembldb’ version 1.6.2

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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