currentEnsemblGenomeBuild | Current genome build |
currentEnsemblVersion | Current genome version |
currentFlyBaseVersion | Current genome version |
currentGencodeGenomeBuild | Current genome build |
currentGencodeVersion | Current genome version |
currentGenomeBuild | Current genome build |
currentGenomeVersion | Current genome version |
currentRefSeqGenomeBuild | Current genome build |
currentRefSeqVersion | Current genome version |
currentUCSCGenomeBuild | Current genome build |
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 |
Ensembl2Ncbi | Ensembl-to-NCBI gene identifier mappings |
Ensembl2Ncbi-class | Ensembl-to-NCBI gene identifier mappings |
Ensembl2Ncbi-method | Ensembl-to-NCBI gene identifier mappings |
EnsemblGenes | Generate an 'EnsemblGenes' object |
EnsemblGenes-class | Ensembl gene annotations |
EnsemblTranscripts-class | Ensembl transcript annotations |
export | Export |
export-method | Export |
FlyBaseGenes-class | FlyBase gene annotations |
FlyBaseTranscripts-class | FlyBase transcript annotations |
GencodeGenes-class | GENCODE gene annotations |
gencodeReleaseHistory | GENCODE release history |
GencodeTranscripts-class | GENCODE transcript annotations |
Gene2Symbol | Gene-to-symbol mappings |
Gene2Symbol-class | Gene-to-symbol mappings |
Gene2Symbol-method | Gene-to-symbol mappings |
HGNC | Import Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC) metadata |
HGNC-class | Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC) metadata |
importTx2Gene | Import transcript-to-gene annotations |
makeEnsDbFromGFF | Make EnsDb object from a GFF/GTF file |
makeGene2Symbol | Make a Gene2Symbol object |
makeGene2SymbolFromEnsDb | Make a Gene2Symbol object |
makeGene2SymbolFromEnsembl | Make a Gene2Symbol object |
makeGene2SymbolFromGFF | Make a Gene2Symbol object |
makeGRangesFromEnsDb | Make genomic ranges ('GRanges') from Ensembl |
makeGRangesFromEnsembl | Make genomic ranges ('GRanges') from Ensembl |
makeGRangesFromGFF | Make genomic ranges ('GRanges') from a GFF/GTF file |
makeProtein2Gene | Map protein identifiers to genes |
makeProtein2GeneFromEnsembl | Map protein identifiers to genes |
makeTx2Gene | Make a Tx2Gene object |
makeTx2GeneFromEnsDb | Make a Tx2Gene object |
makeTx2GeneFromEnsembl | Make a Tx2Gene object |
makeTx2GeneFromFASTA | Make a Tx2Gene object from transcriptome FASTA |
makeTx2GeneFromGFF | Make a Tx2Gene object |
mapEnsemblReleaseToURL | Map Ensembl release to archive URL. |
mapGencodeToEnsembl | Map GENCODE release to Ensembl |
mapGeneNamesToEnsembl | Map gene names to Ensembl |
mapGeneNamesToHGNC | Map gene names (symbols) to HGNC identifiers |
mapGeneNamesToNCBI | Map gene names to NCBI |
mapHumanOrthologs | Map input to human gene orthologs |
MGI | Import Mouse Genome Informatics (MGI) metadata |
MGI-class | Mouse Genomic Informatics (MGI) metadata |
Ncbi2Ensembl | NCBI-to-Ensembl gene identifier mappings |
Ncbi2Ensembl-class | NCBI-to-Ensembl gene identifier mappings |
Ncbi2Ensembl-method | NCBI-to-Ensembl gene identifier mappings |
NcbiGeneInfo | Import NCBI (Entrez) gene identifier information |
NcbiGeneInfo-class | NCBI gene identifier information |
organism | Organism |
organism-method | Organism |
organism<- | Organism |
organism<--method | Organism |
Protein2Gene-class | Protein-to-gene mappings |
RefSeqGenes-class | RefSeq gene annotations |
RefSeqTranscripts-class | RefSeq transcript annotations |
show | Show an object |
show-method | Show an object |
stripGeneVersions | Strip gene identifier versions |
stripGeneVersions-method | Strip gene identifier versions |
stripTranscriptVersions | Strip transcript identifier versions |
stripTranscriptVersions-method | Strip transcript identifier versions |
Tx2Gene | Transcript-to-gene mappings |
Tx2Gene-class | Transcript-to-gene mappings |
Tx2Gene-method | Transcript-to-gene mappings |
UCSCGenes-class | UCSC gene annotations |
UCSCTranscripts-class | UCSC transcript annotations |
updateObject | Update object |
updateObject-method | Update object |
WormBaseGenes-class | WormBase gene annotations |
WormBaseTranscripts-class | WormBase transcript annotations |