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All functions

Ensembl2Entrez-class
Ensembl-to-Entrez gene identifier mappings
Ensembl2Entrez()
Ensembl-to-Entrez gene identifier mappings
EnsemblGenes-class
Ensembl gene annotations
EnsemblTranscripts-class
Ensembl transcript annotations
Entrez2Ensembl-class
Entrez-to-Ensembl gene identifier mappings
Entrez2Ensembl()
Entrez-to-Ensembl gene identifier mappings
EntrezGeneInfo-class
NCBI Entrez gene identifier information
EntrezGeneInfo()
Import NCBI Entrez gene identifier information
FlyBaseGenes-class
FlyBase gene annotations
FlyBaseTranscripts-class
FlyBase transcript annotations
GencodeGenes-class
GENCODE gene annotations
GencodeTranscripts-class
GENCODE transcript annotations
Gene2Symbol-class
Gene-to-symbol mappings
Gene2Symbol()
Gene-to-symbol mappings
HGNC-class
HGNC complete set metadata
HGNC()
Import HGNC complete set metadata
HGNC2Ensembl-class
HGNC-to-Ensembl gene identifier mappings
HGNC2Ensembl()
HGNC-to-Ensembl gene identifier mappings
MGI2Ensembl-class
MGI-to-Ensembl gene identifier mappings
MGI2Ensembl()
MGI-to-Ensembl gene identifier mappings
Protein2Gene-class
Protein-to-gene mappings
RefSeqGenes-class
RefSeq gene annotations
RefSeqTranscripts-class
RefSeq transcript annotations
Tx2Gene-class
Transcript-to-gene mappings
Tx2Gene()
Transcript-to-gene mappings
UCSCGenes-class
UCSC gene annotations
UCSCTranscripts-class
UCSC transcript annotations
WormBaseGenes-class
WormBase gene annotations
WormBaseTranscripts-class
WormBase transcript annotations
currentEnsemblGenomeBuild() currentGencodeGenomeBuild() currentRefSeqGenomeBuild() currentUCSCGenomeBuild()
Current genome build
currentEnsemblVersion() currentGencodeVersion() currentRefSeqVersion() currentFlyBaseVersion() currentWormBaseVersion()
Current genome version
detectOrganism()
Detect organism
downloadEnsemblGenome()
Download Ensembl reference genome
downloadGencodeGenome()
Download GENCODE reference genome
downloadRefSeqGenome()
Download RefSeq reference genome
downloadUCSCGenome()
Download UCSC reference genome
emptyRanges()
Generate empty genomic ranges
export()
Export
geneSynonyms()
Gene synonyms
importTx2Gene()
Import transcript-to-gene annotations
makeEnsDbFromGFF()
Make EnsDb object from a GFF/GTF file
makeGRangesFromEnsembl() makeGRangesFromEnsDb()
Make GenomicRanges from Ensembl
makeGRangesFromGFF()
Make GenomicRanges from a GFF/GTF file
makeGene2SymbolFromEnsembl() makeGene2SymbolFromEnsDb() makeGene2SymbolFromGFF()
Make a Gene2Symbol object
makeProtein2GeneFromEnsembl()
Map protein identifiers to genes
makeTx2GeneFromEnsembl() makeTx2GeneFromEnsDb() makeTx2GeneFromGFF()
Make a Tx2Gene object
makeTx2GeneFromFASTA()
Make a Tx2Gene object from transcriptome FASTA
mapEnsemblReleaseToURL()
Map Ensembl release to archive URL.
mapGencodeToEnsembl()
Map GENCODE release to Ensembl
mapHumanOrthologs()
Map input to human gene orthologs
organism() `organism<-`()
Organism
stripGeneVersions()
Strip gene identifier versions
stripTranscriptVersions()
Strip transcript identifier versions