ensembldb
Utilities to create and use Ensembl-based annotation databases

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289
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47
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26
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ensembldb: Utilities to create and use Ensembl-based annotation databases
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API for ensembldb
Utilities to create and use Ensembl-based annotation databases

Global functions
.AnnotationFilterClassNames Source code
.ProteinsFromDataframe Source code
.abbrevOrganismName Source code
.activeFilter Source code
.addFilter Source code
.anyIs Source code
.buildQuery Source code
.cds_for_id Source code
.cds_for_id2 Source code
.cds_for_id_range Source code
.cds_matching_protein Source code
.checkExtractVersions Source code
.checkIntegerCols Source code
.collapseEntrezidInTable Source code
.conditionForEnsDb Source code
.createEnsDbIndices Source code
.dropFilter Source code
.ensVersionFromSourceUrl Source code
.ensdb_protein_tables Source code
.ensdb_tables Source code
.fieldInEnsDb Source code
.fieldToClass Source code
.filterFields Source code
.filterKeytypes Source code
.filter_for_idType Source code
.formatSeqnameByStyleForQuery Source code
.formatSeqnameByStyleFromQuery Source code
.genome_to_tx Source code
.genome_to_tx_ranges Source code
.getColMappings Source code
.getColumns Source code
.getEnsemblMysqlUrl Source code
.getMetaDataValue Source code
.getReadMysqlTable Source code
.getSeqlengthsFromMysqlFolder Source code
.getSeqnameNotFoundOption Source code
.getWhat Source code
.guessDatabaseName Source code
.ids_message Source code
.keytype2FilterMapping Source code
.logOp2SQL Source code
.makeObjectName Source code
.makePackageName Source code
.mapIds Source code
.mysql_datatype Source code
.onLoad Source code
.organismName Source code
.processFilterParam Source code
.proteinCoordsToTx Source code
.queryForEnsDb Source code
.queryForEnsDbWithTables Source code
.reduceAH Source code
.select Source code
.simpleKeytypes Source code
.splice Source code
.supportedFilters Source code
.toSaf Source code
.to_genome Source code
.transcriptLengths Source code
.tx_to_genome Source code
.tx_to_protein Source code
.txs_to_proteins Source code
.valueForEnsDb Source code
Deprecated Man page
EnsDb Man page Source code
EnsDb-class Man page
EntrezidFilter Man page Source code
ExonidFilter Man page Source code
ExonrankFilter Man page Source code
Filter-classes Man page
GenebiotypeFilter Man page Source code
GeneidFilter Man page Source code
OnlyCodingTxFilter Man page Source code
OnlyCodingTxFilter-class Man page
ProtDomIdFilter Man page Source code
ProtDomIdFilter-class Man page
ProteinDomainIdFilter Man page Source code
ProteinDomainIdFilter-class Man page
ProteinDomainSourceFilter Man page Source code
ProteinDomainSourceFilter-class Man page
SQLiteName2MySQL Source code
SeqendFilter Man page Source code
SeqnameFilter Man page Source code
SeqstartFilter Man page Source code
SeqstrandFilter Man page Source code
TxSupportLevelFilter Man page Source code
TxSupportLevelFilter-class Man page
TxbiotypeFilter Man page Source code
TxidFilter Man page Source code
UniprotDbFilter Man page Source code
UniprotDbFilter-class Man page
UniprotMappingTypeFilter Man page Source code
UniprotMappingTypeFilter-class Man page
activeFilter Man page
activeFilter,EnsDb-method Man page
addFilter Man page
addFilter,EnsDb-method Man page
addFilterColumns Source code
addRequiredTables Source code
anyProteinColumns Source code
buildMetadata Source code
buildWhereForGRanges Source code
cdsBy Man page
cdsBy,EnsDb-method Man page
cdsToTranscript Man page Source code
checkOrderBy Source code
checkValidEnsDb Source code
columns,EnsDb-method Man page
compareChromosomes Source code
compareEnsDbs Source code
compareExons Source code
compareGenes Source code
compareProteins Source code
compareTx Source code
convertFilter,AnnotationFilter,EnsDb-method Man page
convertFilter,AnnotationFilterList,EnsDb-method Man page
dbHasRequiredTables Source code
dbHasValidTables Source code
dbSchemaVersion Source code
dbconn Man page
dbconn,EnsDb-method Man page
disjointExons,EnsDb-method Man page
dropFilter Man page
dropFilter,EnsDb-method Man page
dropProperty Source code
elementFromEnsemblFilename Source code
ensDbColumnForColumn Source code
ensDbFromAH Man page Source code
ensDbFromGRanges Man page Source code
ensDbFromGff Man page Source code
ensDbFromGtf Man page Source code
ensemblVersion Man page
ensemblVersion,EnsDb-method Man page
ensemblVersionFromGtfFileName Source code
ensembldb-deprecated Man page
exons Man page
exons,EnsDb-method Man page
exonsBy Man page
exonsBy,EnsDb-method Man page
exonsByOverlaps,EnsDb-method Man page
feedEnsDb2MySQL Source code
fetchTablesFromEnsembl Man page Source code
filter Man page Source code
filterForKeytype Source code
fiveUTRsByTranscript,EnsDb-method Man page
fixCDStypeInEnsemblGTF Source code
genes Man page
genes,EnsDb-method Man page
genomeToProtein Man page Source code
genomeToTranscript Man page Source code
genomeVersionFromGtfFileName Source code
getGeneRegionTrackForGviz Man page
getGeneRegionTrackForGviz,EnsDb-method Man page
getGenomeFaFile Man page
getGenomeFaFile,EnsDb-method Man page
getGenomeTwoBitFile Man page
getGenomeTwoBitFile,EnsDb-method Man page
getUTRsByTranscript Source code
hasProteinData Man page
hasProteinData,EnsDb-method Man page
intronsByTranscript,EnsDb-method Man page
isEnsemblFileName Source code
isProteinFilter Source code
joinQueryOnColumns2 Source code
joinQueryOnTables2 Source code
joinTwoTables Source code
keys,EnsDb-method Man page
keytypes,EnsDb-method Man page
lengthOf Man page
lengthOf,EnsDb-method Man page
lengthOf,GRangesList-method Man page
listColumns Man page
listColumns,EnsDb-method Man page
listEnsDbs Man page Source code
listGenebiotypes Man page
listGenebiotypes,EnsDb-method Man page
listProteinColumns Man page Source code
listTables Man page
listTables,EnsDb-method Man page
listTxbiotypes Man page
listTxbiotypes,EnsDb-method Man page
listUniprotDbs Man page
listUniprotDbs,EnsDb-method Man page
listUniprotMappingTypes Man page
listUniprotMappingTypes,EnsDb-method Man page
makeEnsemblSQLiteFromTables Man page Source code
makeEnsembldbPackage Man page Source code
mapIds,EnsDb-method Man page
metadata Man page
metadata,EnsDb-method Man page
num2strand Source code
orderDataFrameBy Source code
organism Man page
organism,EnsDb-method Man page
organismFromGtfFileName Source code
prefixChromName Source code
prefixColumns Source code
prefixColumnsKeepOrder Source code
promoters Man page
promoters,EnsDb-method Man page
proteinToGenome Man page Source code
proteinToTranscript Man page Source code
proteins Man page
proteins,EnsDb-method Man page
removePrefix Source code
returnFilterColumns Man page
returnFilterColumns,EnsDb-method Man page
returnFilterColumns<- Man page
returnFilterColumns<-,EnsDb-method Man page
runEnsDbApp Man page Source code
select Man page
select,EnsDb-method Man page
seqinfo Man page
seqinfo,EnsDb-method Man page
seqlevels Man page
seqlevels,EnsDb-method Man page
seqlevels,GRangesFilter-method Man page
seqlevelsStyle Man page
seqlevelsStyle,EnsDb-method Man page
seqlevelsStyle<- Man page
seqlevelsStyle<-,EnsDb-method Man page
seqnames,GRangesFilter-method Man page
setFeatureInGRangesFilter Source code
show Man page
show,EnsDb-method Man page
strand2num Source code
supportedFilters,EnsDb-method Man page
supportedSeqlevelsStyles Man page
supportedSeqlevelsStyles,EnsDb-method Man page
threeUTRsByTranscript,EnsDb-method Man page
toSAF Man page
toSAF,GRangesList-method Man page
transcriptLengths Man page
transcriptLengths,EnsDb-method Man page
transcriptLengths,TxDb-method Man page
transcriptToCds Man page Source code
transcriptToGenome Man page Source code
transcriptToProtein Man page Source code
transcripts Man page
transcripts,EnsDb-method Man page
transcriptsBy Man page
transcriptsBy,EnsDb-method Man page
transcriptsByOverlaps,EnsDb-method Man page
tryGetSeqinfoFromEnsembl Source code
ucscToEns Source code
ucscToEnsMapping Source code
updateEnsDb Man page
updateEnsDb,EnsDb-method Man page
useMySQL Man page
useMySQL,EnsDb-method Man page
validateEnsDb Source code
ensembldb documentation built on Nov. 8, 2020, 4:57 p.m.

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