Acid Genomics Genome Annotations

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Documentation for package ‘AcidGenomes’ version 0.7.0

• DESCRIPTION file.
• Package NEWS.

Help Pages

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
EnsemblGenes	Generate an 'EnsemblGenes' object
EnsemblGenes-class	Ensembl gene annotations
EnsemblToNcbi	Ensembl-to-NCBI gene identifier mappings
EnsemblToNcbi-class	Ensembl-to-NCBI gene identifier mappings
EnsemblToNcbi-method	Ensembl-to-NCBI gene identifier mappings
EnsemblTranscripts-class	Ensembl transcript annotations
export	Export data from R
export-method	Export data from R
FlybaseGenes-class	FlyBase gene annotations
FlybaseTranscripts-class	FlyBase transcript annotations
GencodeGenes-class	GENCODE gene annotations
gencodeReleaseHistory	GENCODE release history
GencodeTranscripts-class	GENCODE transcript annotations
GeneToSymbol	Gene-to-symbol mappings
GeneToSymbol-class	Gene-to-symbol mappings
GeneToSymbol-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
importTxToGene	Import transcript-to-gene annotations
JaxHumanToMouse	Import human-to-mouse gene mappings from the Jackson Laboratory (JAX) Mouse Genome Informatics (MGI) website
JaxHumanToMouse-class	Jackson Laboratory (JAX) human-to-mouse gene mappings
makeEnsDbFromGff	Make EnsDb object from a GFF/GTF file
makeGeneToSymbol	Make a GeneToSymbol object
makeGeneToSymbolFromEnsDb	Make a GeneToSymbol object
makeGeneToSymbolFromEnsembl	Make a GeneToSymbol object
makeGeneToSymbolFromGff	Make a GeneToSymbol 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
makeProteinToGene	Map protein identifiers to genes
makeProteinToGeneFromEnsembl	Map protein identifiers to genes
makeTxToGene	Make a TxToGene object
makeTxToGeneFromEnsDb	Make a TxToGene object
makeTxToGeneFromEnsembl	Make a TxToGene object
makeTxToGeneFromFasta	Make a TxToGene object from transcriptome FASTA
makeTxToGeneFromGff	Make a TxToGene 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
NcbiGeneHistory	NCBI gene history
NcbiGeneHistory-class	NCBI gene history
NcbiGeneInfo	Import NCBI (Entrez) gene identifier information
NcbiGeneInfo-class	NCBI gene identifier information
NcbiToEnsembl	NCBI-to-Ensembl gene identifier mappings
NcbiToEnsembl-class	NCBI-to-Ensembl gene identifier mappings
NcbiToEnsembl-method	NCBI-to-Ensembl gene identifier mappings
organism	Organism
organism-method	Organism
organism<-	Organism
organism<--method	Organism
ProteinToGene-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
TxToGene	Transcript-to-gene mappings
TxToGene-class	Transcript-to-gene mappings
TxToGene-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