All functions

Ensembl2Entrez-class

Ensembl-to-Entrez gene identifier mappings

Ensembl2Entrez() Entrez2Ensembl()

Ensembl-to-Entrez gene identifier mappings

EnsemblGenes-class

Ensembl gene annotations

EnsemblTranscripts-class

Ensembl transcript annotations

Entrez2Ensembl-class

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 identifier mappings

Tx2Gene()

Transcript-to-gene identifier 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(<Tx2Gene>)

Export

geneSynonyms()

Gene synonyms

getEnsDb()

Get EnsDb from Bioconductor

getGFFDirectives()

Get the directives from a GFF file

getGFFMetadata()

Get metadata about a GFF file

importTx2Gene()

Import transcript-to-gene annotations

makeEnsDbFromGFF()

Make EnsDb object from a GFF/GTF file

makeGRangesFromEnsembl() makeGRangesFromEnsDb() annotable()

Make GRanges from Ensembl

makeGRangesFromGFF()

Make GRanges from a GFF/GTF file

makeGRangesFromTxDb()

Make GRanges from TxDb object

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

makeTxDbFromGFF()

Make TxDb from a GFF/GTF file

mapEnsemblReleaseToURL()

Map Ensembl release to archive URL.

mapUCSCBuildToEnsembl() mapEnsemblBuildToUCSC()

Interconvert between EBI (Ensembl), NCBI, and UCSC genome build names

mapHumanOrthologs()

Map input to human gene orthologs

organism() `organism<-`()

Organism

stripGeneVersions() stripTranscriptVersions()

Strip transcript identifier versions