Function reference • AcidGenomes

All functions

EnsemblGenes-class: Ensembl gene annotations

EnsemblGenes(): Generate an EnsemblGenes object

EnsemblToNcbi-class: Ensembl-to-NCBI gene identifier mappings

EnsemblToNcbi(): Ensembl-to-NCBI gene identifier mappings

EnsemblTranscripts-class: Ensembl transcript annotations

FlybaseGenes-class: FlyBase gene annotations

FlybaseTranscripts-class: FlyBase transcript annotations

GencodeGenes-class: GENCODE gene annotations

GencodeTranscripts-class: GENCODE transcript annotations

GeneToSymbol-class: Gene-to-symbol mappings

GeneToSymbol(): Gene-to-symbol mappings

Hgnc-class: Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC) metadata

Hgnc(): Import Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC) metadata

JaxHumanToMouse-class: Jackson Laboratory (JAX) human-to-mouse gene mappings

JaxHumanToMouse(): Import human-to-mouse gene mappings from the Jackson Laboratory (JAX) Mouse Genome Informatics (MGI) website

Mgi-class: Mouse Genomic Informatics (MGI) metadata

Mgi(): Import Mouse Genome Informatics (MGI) metadata

NcbiGeneHistory-class: NCBI gene history

NcbiGeneHistory(): NCBI gene history

NcbiGeneInfo-class: NCBI gene identifier information

NcbiGeneInfo(): Import NCBI (Entrez) gene identifier information

NcbiToEnsembl-class: NCBI-to-Ensembl gene identifier mappings

NcbiToEnsembl(): NCBI-to-Ensembl gene identifier mappings

ProteinToGene-class: Protein-to-gene mappings

RefseqGenes-class: RefSeq gene annotations

RefseqTranscripts-class: RefSeq transcript annotations

TxToGene-class: Transcript-to-gene mappings

TxToGene(): Transcript-to-gene 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(): Export data from R

gencodeReleaseHistory(): GENCODE release history

importTxToGene(): Import transcript-to-gene annotations

makeEnsDbFromGff(): Make EnsDb object from a GFF/GTF file

makeGRangesFromEnsembl() makeGRangesFromEnsDb(): Make genomic ranges (GRanges) from Ensembl

makeGRangesFromGff(): Make genomic ranges (GRanges) from a GFF/GTF file

makeGeneToSymbolFromEnsembl() makeGeneToSymbolFromEnsDb() makeGeneToSymbolFromGff(): Make a GeneToSymbol object

makeProteinToGeneFromEnsembl(): Map protein identifiers to genes

makeTxToGeneFromEnsembl() makeTxToGeneFromEnsDb() makeTxToGeneFromGff(): Make a TxToGene object

makeTxToGeneFromFasta(): Make a TxToGene object from transcriptome FASTA

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

organism() `organism<-`(): Organism

show(): Show an object

stripGeneVersions(): Strip gene identifier versions

stripTranscriptVersions(): Strip transcript identifier versions

updateObject(): Update object