Utilities to create and use an Ensembl based annotation database

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Documentation for package ‘ensembldb’ version 1.2.2

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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
column Filter results fetched from the Ensembl database
column-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
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
EnsDb Basic usage of an Ensembl based annotation database
EnsDb-class Basic usage of an Ensembl based annotation database
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
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
fetchTablesFromEnsembl Generating a Ensembl annotation package from Ensembl
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
getGenomeFaFile Retrieve annotation data from an Ensembl based package
getGenomeFaFile-method Retrieve annotation data from an Ensembl based package
lengthOf Basic usage of an Ensembl based annotation database
lengthOf-method Basic usage of an Ensembl based annotation database
listColumns Basic usage of an Ensembl based annotation database
listColumns-method Basic usage of an Ensembl based annotation database
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
makeEnsembldbPackage Generating a Ensembl annotation package from Ensembl
makeEnsemblSQLiteFromTables Generating a Ensembl annotation package from Ensembl
metadata Basic usage of an Ensembl based annotation database
metadata-method Basic usage of an Ensembl based annotation database
organism Basic usage of an Ensembl based annotation database
organism-method Basic usage of an Ensembl based annotation database
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
runEnsDbApp Search annotations interactively
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
SeqnameFilter Constructor functions for filter objects
SeqnameFilter-class 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
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
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
where Filter results fetched from the Ensembl database
where-method Filter results fetched from the Ensembl database