Package index • AcidGenomes

Download genome files

downloadEnsemblGenome(): Download Ensembl reference genome
downloadGencodeGenome(): Download GENCODE reference genome
downloadRefseqGenome(): Download RefSeq reference genome
downloadUcscGenome(): Download UCSC reference genome

Current versions and builds

currentEnsemblGenomeBuild() currentGencodeGenomeBuild() currentRefseqGenomeBuild() currentUcscGenomeBuild(): Current genome build
currentEnsemblVersion() currentGencodeVersion() currentRefseqVersion() currentFlybaseVersion() currentWormbaseVersion(): Current genome version
gencodeReleaseHistory(): GENCODE release history
detectOrganism(): Detect organism

Make genomic objects

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
makeProteinToGeneFromEnsembl(): Map protein identifiers to genes
makeTxToGeneFromFasta(): Make a TxToGene object from transcriptome FASTA
EnsemblGenes(): Generate an EnsemblGenes object
EnsemblToNcbi(): Ensembl-to-NCBI gene identifier mappings
GeneToSymbol(): Gene-to-symbol mappings
Hgnc(): Import Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC) metadata
JaxHumanToMouse(): Import human-to-mouse gene mappings from the Jackson Laboratory (JAX) Mouse Genome Informatics (MGI) website
Mgi(): Import Mouse Genome Informatics (MGI) metadata
NcbiGeneHistory(): NCBI gene history
NcbiGeneInfo(): Import NCBI (Entrez) gene identifier information
NcbiToEnsembl(): NCBI-to-Ensembl gene identifier mappings
TxToGene(): Transcript-to-gene mappings

Gene name mapping

mapEnsemblReleaseToUrl(): Map Ensembl release to archive URL.
mapEnsemblToGencode(): Map Ensembl release to GENCODE
mapGencodeToEnsembl(): Map GENCODE release to Ensembl
mapGeneNamesToEnsembl(): Map gene names to Ensembl identifiers
mapGeneNamesToHgnc(): Map gene names (symbols) to HGNC identifiers
mapGeneNamesToNcbi(): Map gene names to NCBI
mapGenesToOmim(): Map gene identifiers to OMIM disease identifiers
mapGoTerms(): Map gene ontology (GO) identifiers to term names
mapHumanOrthologs(): Map input to human gene orthologs
mapHumanToMouse(): Map human gene names to mouse orthologs
mapRnacentral(): Import RNAcentral identifier mappings
goTermsPerGeneName(): Import gene ontology (GO) terms per gene name

Version and ID utilities

stripExonVersions(): Strip exon identifier versions
stripGeneVersions(): Strip gene identifier versions
stripTranscriptVersions(): Strip transcript identifier versions
mapEnsemblReleaseToUrl(): Map Ensembl release to archive URL.
mapEnsemblToGencode(): Map Ensembl release to GENCODE
mapGencodeToEnsembl(): Map GENCODE release to Ensembl
updateGeneSymbols(): Update gene symbols
emptyRanges(): Generate empty genomic ranges

Data access

getEnsDb(): Get EnsDb from Bioconductor
export(): Export data from R
importTxToGene(): Import transcript-to-gene annotations
AcidGenomesTestsUrl: AcidGenomes test data URL

Internal

EnsemblCds-class: Ensembl CDS (coding sequence) annotations
EnsemblExons-class: Ensembl exon annotations
EnsemblGenes-class: Ensembl gene annotations
EnsemblToNcbi-class: Ensembl-to-NCBI gene identifier mappings
EnsemblTranscripts-class: Ensembl transcript annotations
FlybaseExons-class: FlyBase exon annotations
FlybaseGenes-class: FlyBase gene annotations
FlybaseTranscripts-class: FlyBase transcript annotations
GencodeExons-class: GENCODE exon annotations
GencodeGenes-class: GENCODE gene annotations
GencodeTranscripts-class: GENCODE transcript annotations
GeneToSymbol-class: Gene-to-symbol mappings
Hgnc-class: Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC) metadata
JaxHumanToMouse-class: Jackson Laboratory (JAX) human-to-mouse gene mappings
Mgi-class: Mouse Genomic Informatics (MGI) metadata
NcbiGeneHistory-class: NCBI gene history
NcbiGeneInfo-class: NCBI gene identifier information
NcbiToEnsembl-class: NCBI-to-Ensembl gene identifier mappings
ProteinToGene-class: Protein-to-gene mappings
RefseqExons-class: RefSeq exon annotations
RefseqGenes-class: RefSeq gene annotations
RefseqTranscripts-class: RefSeq transcript annotations
TxToGene-class: Transcript-to-gene mappings
UcscExons-class: UCSC exon annotations
UcscGenes-class: UCSC gene annotations
UcscTranscripts-class: UCSC transcript annotations
WormbaseExons-class: WormBase exon annotations
WormbaseGenes-class: WormBase gene annotations
WormbaseTranscripts-class: WormBase transcript annotations
importEnsemblToNcbiGeneMap(): Import Ensembl-to-NCBI gene identifier mappings
organism() `organism<-`(): Organism
show(): Show an object
updateObject(): Update object