Acid Genomics Genome Annotations

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Documentation for package ‘AcidGenomes’ version 0.2.13

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annotable Make GRanges from Ensembl
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
Ensembl2Entrez Ensembl-to-Entrez gene identifier mappings
Ensembl2Entrez-class Ensembl-to-Entrez gene identifier mappings
Ensembl2Entrez-method Ensembl-to-Entrez gene identifier mappings
EnsemblGenes-class Ensembl gene annotations
EnsemblTranscripts-class Ensembl transcript annotations
Entrez2Ensembl Ensembl-to-Entrez gene identifier mappings
Entrez2Ensembl-class Entrez-to-Ensembl gene identifier mappings
Entrez2Ensembl-method Ensembl-to-Entrez gene identifier mappings
EntrezGeneInfo Import NCBI Entrez gene identifier information
EntrezGeneInfo-class NCBI Entrez gene identifier information
export Export
export-method Export
FlyBaseGenes-class FlyBase gene annotations
FlyBaseTranscripts-class FlyBase transcript annotations
GencodeGenes-class GENCODE gene annotations
GencodeTranscripts-class GENCODE transcript annotations
Gene2Symbol Gene-to-symbol mappings
Gene2Symbol-class Gene-to-symbol mappings
Gene2Symbol-method Gene-to-symbol mappings
geneSynonyms Gene synonyms
getEnsDb Get EnsDb from Bioconductor
getGFFDirectives Get the directives from a GFF file
getGFFMetadata Get metadata about a GFF file
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
makeEnsDbFromGFF Make EnsDb object from a GFF/GTF file
makeGene2Symbol Make a Gene2Symbol object
makeGene2SymbolFromEnsDb Make a Gene2Symbol object
makeGene2SymbolFromEnsembl Make a Gene2Symbol object
makeGene2SymbolFromGFF Make a Gene2Symbol object
makeGRangesFromEnsDb Make GRanges from Ensembl
makeGRangesFromEnsembl Make GRanges from Ensembl
makeGRangesFromGFF Make GRanges from a GFF/GTF file
makeGRangesFromTxDb Make GRanges from TxDb object
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
makeTxDbFromGFF Make TxDb from a GFF/GTF file
mapEnsemblBuildToUCSC Interconvert between EBI (Ensembl), NCBI, and UCSC genome build names
mapEnsemblReleaseToURL Map Ensembl release to archive URL.
mapGenomeBuild Interconvert between EBI (Ensembl), NCBI, and UCSC genome build names
mapHumanOrthologs Map input to human gene orthologs
mapUCSCBuildToEnsembl Interconvert between EBI (Ensembl), NCBI, and UCSC genome build names
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
RefSeqGenes-class RefSeq gene annotations
RefSeqTranscripts-class RefSeq transcript annotations
stripGeneVersions Strip transcript identifier versions
stripGeneVersions-method Strip transcript identifier versions
stripTranscriptVersions Strip transcript identifier versions
stripTranscriptVersions-method Strip transcript identifier versions
stripVersions Strip transcript identifier versions
Tx2Gene Transcript-to-gene identifier mappings
Tx2Gene-class Transcript-to-gene identifier mappings
Tx2Gene-method Transcript-to-gene identifier mappings
UCSCGenes-class UCSC gene annotations
UCSCTranscripts-class UCSC transcript annotations
WormBaseGenes-class WormBase gene annotations
WormBaseTranscripts-class WormBase transcript annotations