API for jotsetung/ensembldb
Utilities to create and use Ensembl-based annotation databases

Global functions
AnnotationFilterClassNames 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
ProteinsFromDataframe Source code
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
abbrevOrganismName Source code
activeFilter Man page Source code
activeFilter,EnsDb-method Man page
addFilter Man page Source code
addFilter,EnsDb-method Man page
addFilterColumns Source code
addRequiredTables Source code
anyIs Source code
anyProteinColumns Source code
buildMetadata Source code
buildQuery Source code
buildWhereForGRanges Source code
cdsBy Man page
cdsBy,EnsDb-method Man page
cdsToTranscript Man page Source code
cds_for_id Source code
cds_for_id_range Source code
cds_matching_protein Source code
checkExtractVersions Source code
checkIntegerCols Source code
checkOrderBy Source code
checkValidEnsDb Source code
collapseEntrezidInTable 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
conditionForEnsDb Source code
convertFilter,AnnotationFilter,EnsDb-method Man page
convertFilter,AnnotationFilterList,EnsDb-method Man page
createEnsDbIndices Source code
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 Source code
dropFilter,EnsDb-method Man page
dropProperty Source code
ds_message 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
ensVersionFromSourceUrl Source code
ensdb_protein_tables Source code
ensdb_tables 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
extractTranscriptSeqs Man page
extractTranscriptSeqs,ANY,ANY Man page
extractTranscriptSeqs,ANY,EnsDb-method Man page
extractTranscriptSeqs,ANY-method Man page
feedEnsDb2MySQL Source code
fetchTablesFromEnsembl Man page Source code
fieldInEnsDb Source code
fieldToClass Source code
filter Man page Source code
filterFields Source code
filterForKeytype Source code
filterKeytypes Source code
filter_for_idType Source code
fiveUTRsByTranscript,EnsDb-method Man page
fixCDStypeInEnsemblGTF Source code
formatSeqnameByStyleForQuery Source code
formatSeqnameByStyleFromQuery Source code
genes Man page
genes,EnsDb-method Man page
genomeToProtein Man page Source code
genomeToTranscript Man page Source code
genomeVersionFromGtfFileName Source code
genome_to_tx Source code
getColMappings Source code
getColumns Source code
getEnsemblMysqlUrl Source code
getGeneRegionTrackForGviz Man page
getGeneRegionTrackForGviz,EnsDb-method Man page
getGenomeFaFile Man page
getGenomeFaFile,EnsDb-method Man page
getMetaDataValue Source code
getReadMysqlTable Source code
getSeqlengthsFromMysqlFolder Source code
getSeqnameNotFoundOption Source code
getUTRsByTranscript Source code
getWhat Source code
guessDatabaseName Source code
hasProteinData Man page
hasProteinData,EnsDb-method Man page
isEnsemblFileName Source code
isProteinFilter Source code
joinQueryOnColumns2 Source code
joinQueryOnTables2 Source code
joinTwoTables Source code
keys,EnsDb-method Man page
keytype2FilterMapping Source code
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
logOp2SQL Source code
makeEnsemblSQLiteFromTables Man page Source code
makeEnsembldbPackage Man page Source code
makeObjectName Source code
makePackageName Source code
mapIds Source code
mapIds,EnsDb-method Man page
metadata Man page
metadata,EnsDb-method Man page
mysql_datatype Source code
num2strand Source code
onLoad Source code
orderDataFrameBy Source code
organism Man page
organism,EnsDb-method Man page
organismFromGtfFileName Source code
organismName Source code
prefixChromName Source code
prefixColumns Source code
prefixColumnsKeepOrder Source code
processFilterParam Source code
promoters Man page
promoters,EnsDb-method Man page
proteinCoordsToTx Source code
proteinToGenome Man page Source code
proteinToTranscript Man page Source code
proteins Man page
proteins,EnsDb-method Man page
queryForEnsDb Source code
queryForEnsDbWithTables Source code
reduceAH Source code
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 Source code
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
simpleKeytypes Source code
splice Source code
strand2num Source code
supportedFilters 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
toSaf Source code
to_genome Source code
transcriptLengths Man page Source code
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
tx_to_genome Source code
tx_to_protein Source code
txs_to_proteins 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
valueForEnsDb Source code
jotsetung/ensembldb documentation built on Dec. 9, 2018, 10:15 a.m.