Acid Genomics Genome Annotations

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Documentation for package ‘AcidGenomes’ version 0.5.0

• DESCRIPTION file.

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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