Man pages for acidgenomics/AcidGenomes
Acid Genomics Genome Annotations
| AcidGenomes-package | AcidGenomes |
| AcidGenomesTestsUrl | AcidGenomes test data URL |
| currentGenomeBuild | Current genome build |
| currentGenomeVersion | 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 |
| EnsemblTranscripts-class | Ensembl transcript annotations |
| export | 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 |
| Hgnc | Import Human Genome Organization (HUGO) Gene Nomenclature... |
| Hgnc-class | Human Genome Organization (HUGO) Gene Nomenclature Committee... |
| importTxToGene | Import transcript-to-gene annotations |
| JaxHumanToMouse | Import human-to-mouse gene mappings from the Jackson... |
| JaxHumanToMouse-class | Jackson Laboratory (JAX) human-to-mouse gene mappings |
| makeEnsDbFromGff | Make EnsDb object from a GFF/GTF file |
| makeGeneToSymbol | Make a GeneToSymbol object |
| makeGRangesFromEnsembl | Make genomic ranges ('GRanges') from Ensembl |
| makeGRangesFromGff | Make genomic ranges ('GRanges') from a GFF/GTF file |
| makeProteinToGene | Map protein identifiers to genes |
| makeTxToGene | 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 |
| 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 |
| organism | Organism |
| params | Shared parameter documentation |
| ProteinToGene-class | Protein-to-gene mappings |
| RefseqGenes-class | RefSeq gene annotations |
| RefseqTranscripts-class | RefSeq transcript annotations |
| show | Show an object |
| stripGeneVersions | Strip gene identifier versions |
| stripTranscriptVersions | Strip transcript identifier versions |
| summary | Object summaries |
| TxToGene | Transcript-to-gene mappings |
| TxToGene-class | Transcript-to-gene mappings |
| UcscGenes-class | UCSC gene annotations |
| UcscTranscripts-class | UCSC transcript annotations |
| updateObject | Update object |
| WormbaseGenes-class | WormBase gene annotations |
| WormbaseTranscripts-class | WormBase transcript annotations |
