Utilities to create and use Ensembl-based annotation databases

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Documentation for package ‘ensembldb’ version 2.12.1

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A C D E F G H I 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
getGenomeTwoBitFile Functionality related to DNA/RNA sequences
getGenomeTwoBitFile-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

-- I --

intronsByTranscript-method Retrieve annotation data from an Ensembl based package

-- 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 MariaDB/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 MariaDB/MySQL backend
useMySQL-method Use a MariaDB/MySQL backend