Man pages for acidgenomics/AcidGenomes
Acid Genomics Genome Annotations

AcidGenomes-packageAcidGenomes
AcidGenomesTestsURLAcidGenomes test data URL
currentGenomeBuildCurrent genome build
currentGenomeVersionCurrent genome version
detectOrganismDetect organism
downloadEnsemblGenomeDownload Ensembl reference genome
downloadGencodeGenomeDownload GENCODE reference genome
downloadRefSeqGenomeDownload RefSeq reference genome
downloadUCSCGenomeDownload UCSC reference genome
emptyRangesGenerate empty genomic ranges
Ensembl2EntrezEnsembl-to-Entrez gene identifier mappings
Ensembl2Entrez-classEnsembl-to-Entrez gene identifier mappings
EnsemblGenes-classEnsembl gene annotations
EnsemblTranscripts-classEnsembl transcript annotations
Entrez2Ensembl-classEntrez-to-Ensembl gene identifier mappings
EntrezGeneInfoImport NCBI Entrez gene identifier information
EntrezGeneInfo-classNCBI Entrez gene identifier information
exportExport
FlyBaseGenes-classFlyBase gene annotations
FlyBaseTranscripts-classFlyBase transcript annotations
GencodeGenes-classGENCODE gene annotations
GencodeTranscripts-classGENCODE transcript annotations
Gene2SymbolGene-to-symbol mappings
Gene2Symbol-classGene-to-symbol mappings
geneSynonymsGene synonyms
getEnsDbGet EnsDb from Bioconductor
getGFFDirectivesGet the directives from a GFF file
getGFFMetadataGet metadata about a GFF file
HGNCImport HGNC complete set metadata
HGNC2EnsemblHGNC-to-Ensembl gene identifier mappings
HGNC2Ensembl-classHGNC-to-Ensembl gene identifier mappings
HGNC-classHGNC complete set metadata
importTx2GeneImport transcript-to-gene annotations
makeEnsDbFromGFFMake EnsDb object from a GFF/GTF file
makeGene2SymbolMake a Gene2Symbol object
makeGRangesFromEnsemblMake GRanges from Ensembl
makeGRangesFromGFFMake GRanges from a GFF/GTF file
makeGRangesFromTxDbMake GRanges from TxDb object
makeProtein2GeneMap protein identifiers to genes
makeTx2GeneMake a Tx2Gene object
makeTx2GeneFromFASTAMake a Tx2Gene object from transcriptome FASTA
makeTxDbFromGFFMake TxDb from a GFF/GTF file
mapEnsemblReleaseToURLMap Ensembl release to archive URL.
mapHumanOrthologsMap input to human gene orthologs
MGI2EnsemblMGI-to-Ensembl gene identifier mappings
MGI2Ensembl-classMGI-to-Ensembl gene identifier mappings
organismOrganism
paramsShared parameter documentation
Protein2Gene-classProtein-to-gene mappings
reexportsObjects exported from other packages
RefSeqGenes-classRefSeq gene annotations
RefSeqTranscripts-classRefSeq transcript annotations
stripGeneVersionsStrip gene identifier versions
stripTranscriptVersionsStrip transcript identifier versions
summaryObject summaries
Tx2GeneTranscript-to-gene identifier mappings
Tx2Gene-classTranscript-to-gene identifier mappings
UCSCGenes-classUCSC gene annotations
UCSCTranscripts-classUCSC transcript annotations
WormBaseGenes-classWormBase gene annotations
WormBaseTranscripts-classWormBase transcript annotations
acidgenomics/AcidGenomes documentation built on Sept. 16, 2021, 7:30 p.m.