Acid Genomics Genome Annotations

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Documentation for package ‘AcidGenomes’ version 0.1.1

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annotable Make GRanges from Ensembl
currentEnsemblVersion Current genome version
currentFlyBaseVersion Current genome version
currentGencodeVersion Current genome version
currentGenomeVersion Current genome version
currentRefSeqVersion Current genome version
currentWormBaseVersion Current genome version
detectOrganism Detect organism
emptyRanges Generate empty genomic ranges
Ensembl2Entrez Ensembl-to-Entrez gene identifier mappings
Ensembl2Entrez-class Ensembl-to-Entrez gene identifier mappings
Ensembl2Entrez-method Ensembl-to-Entrez gene identifier mappings
Entrez2Ensembl Ensembl-to-Entrez gene identifier mappings
Entrez2Ensembl-class Entrez-to-Ensembl gene identifier mappings
Entrez2Ensembl-method Ensembl-to-Entrez gene identifier mappings
Gene2Symbol Gene-to-symbol mappings
Gene2Symbol-class Gene-to-symbol mappings
Gene2Symbol-method Gene-to-symbol mappings
geneNames Gene names
geneNames-method Gene names
geneSynonyms Gene synonyms
getEnsDb Get EnsDb from Bioconductor AnnotationHub
HGNC Import HGNC complete set metadata
HGNC-class HGNC complete set metadata
HGNC2Ensembl HGNC-to-Ensembl gene identifier mappings
HGNC2Ensembl-class HGNC-to-Ensembl gene identifier mappings
importTx2Gene Import transcript-to-gene annotations
makeGene2Symbol Make a Gene2Symbol object
makeGene2SymbolFromEnsDb Make a Gene2Symbol object
makeGene2SymbolFromEnsembl Make a Gene2Symbol object
makeGene2SymbolFromGFF Make a Gene2Symbol object
makeGene2SymbolFromGTF Make a Gene2Symbol object
makeGRangesFromEnsDb Make GRanges from EnsDb object
makeGRangesFromEnsembl Make GRanges from Ensembl
makeGRangesFromGFF Make GRanges from a GFF/GTF file
makeGRangesFromGTF Make GRanges from a GFF/GTF file
makeProtein2Gene Map protein identifiers to genes
makeProtein2GeneFromEnsembl Map protein identifiers to genes
makeTx2Gene Make a Tx2Gene object
makeTx2GeneFromEnsDb Make a Tx2Gene object
makeTx2GeneFromEnsembl Make a Tx2Gene object
makeTx2GeneFromFASTA Make a Tx2Gene object from transcriptome FASTA
makeTx2GeneFromGFF Make a Tx2Gene object
makeTx2GeneFromGTF Make a Tx2Gene object
mapEnsemblReleaseToURL Map Ensembl release to archive URL.
mapHumanOrthologs Map input to human gene orthologs
mapUCSCBuildToEnsembl Map UCSC genome build to Ensembl
MGI2Ensembl MGI-to-Ensembl gene identifier mappings
MGI2Ensembl-class MGI-to-Ensembl gene identifier mappings
organism Organism
organism-method Organism
organism<- Organism
organism<--method Organism
Protein2Gene-class Protein-to-gene mappings
stripGeneVersions Strip transcript versions
stripTranscriptVersions Strip transcript versions
stripTranscriptVersions-method Strip transcript versions
Tx2Gene Transcript-to-gene identifier mappings
Tx2Gene-class Transcript-to-gene identifier mappings
Tx2Gene-method Transcript-to-gene identifier mappings