# Acid Genomics Genome Annotations

## 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