Man pages for acidgenomics/r-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
EnsemblGenesGenerate an 'EnsemblGenes' object
EnsemblGenes-classEnsembl gene annotations
EnsemblToNcbiEnsembl-to-NCBI gene identifier mappings
EnsemblToNcbi-classEnsembl-to-NCBI gene identifier mappings
EnsemblTranscripts-classEnsembl transcript annotations
exportExport data from R
FlybaseGenes-classFlyBase gene annotations
FlybaseTranscripts-classFlyBase transcript annotations
GencodeGenes-classGENCODE gene annotations
gencodeReleaseHistoryGENCODE release history
GencodeTranscripts-classGENCODE transcript annotations
GeneToSymbolGene-to-symbol mappings
GeneToSymbol-classGene-to-symbol mappings
HgncImport Human Genome Organization (HUGO) Gene Nomenclature...
Hgnc-classHuman Genome Organization (HUGO) Gene Nomenclature Committee...
importTxToGeneImport transcript-to-gene annotations
JaxHumanToMouseImport human-to-mouse gene mappings from the Jackson...
JaxHumanToMouse-classJackson Laboratory (JAX) human-to-mouse gene mappings
makeEnsDbFromGffMake EnsDb object from a GFF/GTF file
makeGeneToSymbolMake a GeneToSymbol object
makeGRangesFromEnsemblMake genomic ranges ('GRanges') from Ensembl
makeGRangesFromGffMake genomic ranges ('GRanges') from a GFF/GTF file
makeProteinToGeneMap protein identifiers to genes
makeTxToGeneMake a TxToGene object
makeTxToGeneFromFastaMake a TxToGene object from transcriptome FASTA
mapEnsemblReleaseToUrlMap Ensembl release to archive URL.
mapGencodeToEnsemblMap GENCODE release to Ensembl
mapGeneNamesToEnsemblMap gene names to Ensembl
mapGeneNamesToHgncMap gene names (symbols) to HGNC identifiers
mapGeneNamesToNcbiMap gene names to NCBI
mapHumanOrthologsMap input to human gene orthologs
MgiImport Mouse Genome Informatics (MGI) metadata
Mgi-classMouse Genomic Informatics (MGI) metadata
NcbiGeneHistoryNCBI gene history
NcbiGeneHistory-classNCBI gene history
NcbiGeneInfoImport NCBI (Entrez) gene identifier information
NcbiGeneInfo-classNCBI gene identifier information
NcbiToEnsemblNCBI-to-Ensembl gene identifier mappings
NcbiToEnsembl-classNCBI-to-Ensembl gene identifier mappings
organismOrganism
paramsShared parameter documentation
ProteinToGene-classProtein-to-gene mappings
RefseqGenes-classRefSeq gene annotations
RefseqTranscripts-classRefSeq transcript annotations
showShow an object
stripGeneVersionsStrip gene identifier versions
stripTranscriptVersionsStrip transcript identifier versions
summaryObject summaries
TxToGeneTranscript-to-gene mappings
TxToGene-classTranscript-to-gene mappings
UcscGenes-classUCSC gene annotations
UcscTranscripts-classUCSC transcript annotations
updateObjectUpdate object
WormbaseGenes-classWormBase gene annotations
WormbaseTranscripts-classWormBase transcript annotations
acidgenomics/r-acidgenomes documentation built on Jan. 12, 2024, 4:06 a.m.