API for acidgenomics/AcidGenomes
Acid Genomics Genome Annotations

Global functions
.addBroadClass	Source code
.addEnsemblFtpMcols	Source code
.annotationHub	Source code
.applyBroadClass	Source code
.cacheIt	Source code
.downloadEnsemblGenome	Source code
.downloadEnsemblGff	Source code
.downloadEnsemblGtf	Source code
.downloadEnsemblMetadata	Source code
.downloadEnsemblTranscriptome	Source code
.downloadGencodeAnnotation	Source code
.downloadGencodeGenome	Source code
.downloadGencodeMetadata	Source code
.downloadGencodeTranscriptome	Source code
.downloadRefSeqAnnotation	Source code
.downloadRefSeqMetadata	Source code
.downloadRefSeqTranscriptome	Source code
.downloadRefseqGenome	Source code
.downloadUcscAnnotation	Source code
.downloadUcscGenome	Source code
.downloadUcscMetadata	Source code
.downloadUcscTranscriptome	Source code
.downloadUrls	Source code
.encodeMcols	Source code
.ensemblFtpGeneMetadata	Source code
.getEnsDb	Source code
.getEnsDbAnnotationHubId	Source code
.getEnsDbFromAnnotationHub	Source code
.getEnsDbFromPackage	Source code
.getEnsDbMetadata	Source code
.getEnsemblSeqinfo	Source code
.getEnsemblToNcbiFromOrgDb	Source code
.getFun	Source code
.getGencodeSeqinfo	Source code
.getGffDirectives	Source code
.getGffMetadata	Source code
.getNcbiGeneIdsFromRefSeqGff	Source code
.getNcbiGeneIdsFromRefSeqGtf	Source code
.getRefSeqAssemblySummary	Source code
.getRefSeqGenomeUrl	Source code
.getRefSeqSeqinfo	Source code
.getSeqinfo	Source code
.getUcscSeqinfo	Source code
.gffFormat	Source code
.gffGenomeBuild	Source code
.gffProvider	Source code
.importEnsemblNcbiMap	Source code
.includeGeneVersion	Source code
.includeTxVersion	Source code
.includeVersion	Source code
.isSupportedGff	Source code
.locateRefSeqAssemblyReport	Source code
.makeEnsemblToNcbi	Source code
.makeGRanges	Source code
.makeGRangesFromRtracklayer	Source code
.makeGRangesFromTxDb	Source code
.makeTxDbFromGff	Source code
.mapGenomeBuildToUCSC	Source code
.mapOrganismToNcbiTaxId	Source code
.matchGRangesNamesColumn	Source code
.matchNcbiTaxonomicGroup	Source code
.md5	Source code
.nest2	Source code
.rtracklayerEnsemblGenesGff	Source code
.rtracklayerEnsemblGenesGtf	Source code
.rtracklayerEnsemblTranscriptsGff	Source code
.rtracklayerEnsemblTranscriptsGtf	Source code
.rtracklayerFlybaseGenesGtf	Source code
.rtracklayerFlybaseTranscriptsGtf	Source code
.rtracklayerGencodeGenesGff	Source code
.rtracklayerGencodeGenesGtf	Source code
.rtracklayerGencodeTranscriptsGff	Source code
.rtracklayerGencodeTranscriptsGtf	Source code
.rtracklayerRefseqGenesGff	Source code
.rtracklayerRefseqGenesGtf	Source code
.rtracklayerRefseqTranscriptsGff	Source code
.rtracklayerRefseqTranscriptsGtf	Source code
.rtracklayerWormbaseGenesGtf	Source code
.rtracklayerWormbaseTranscriptsGtf	Source code
.sha256	Source code
.showGRanges	Source code
.simpleGenomeBuild	Source code
.splitToCharacterList	Source code
.standardizeMcols	Source code
.updateGRanges	Source code
.validateEnsembl	Source code
.validateFlybase	Source code
.validateGRanges	Source code
.validateGencode	Source code
.validateMetadata	Source code
.validateRefseq	Source code
.validateUcsc	Source code
.validateWormbase	Source code
AcidGenomes	Man page
AcidGenomes-package	Man page
AcidGenomesTestsUrl	Man page
EnsemblGenes	Man page
EnsemblGenes-class	Man page
EnsemblToNcbi	Man page
EnsemblToNcbi,EnsemblGenes-method	Man page
EnsemblToNcbi,GencodeGenes-method	Man page
EnsemblToNcbi,Hgnc-method	Man page
EnsemblToNcbi,Mgi-method	Man page
EnsemblToNcbi,character-method	Man page
EnsemblToNcbi-class	Man page
EnsemblTranscripts-class	Man page
FlybaseGenes-class	Man page
FlybaseTranscripts-class	Man page
GencodeGenes-class	Man page
GencodeTranscripts-class	Man page
GeneToSymbol	Man page
GeneToSymbol,DFrame-method	Man page
GeneToSymbol,GRanges-method	Man page
GeneToSymbol-class	Man page
Hgnc	Man page
Hgnc-class	Man page
JaxHumanToMouse	Man page
JaxHumanToMouse-class	Man page
Mgi	Man page Source code
Mgi-class	Man page
NcbiGeneHistory	Man page
NcbiGeneHistory-class	Man page
NcbiGeneInfo	Man page
NcbiGeneInfo-class	Man page
NcbiToEnsembl	Man page
NcbiToEnsembl,Hgnc-method	Man page
NcbiToEnsembl,Mgi-method	Man page
NcbiToEnsembl,integer-method	Man page
NcbiToEnsembl-class	Man page
ProteinToGene-class	Man page
RefseqGenes-class	Man page
RefseqTranscripts-class	Man page
TxToGene	Man page
TxToGene,DFrame-method	Man page
TxToGene,GRanges-method	Man page
TxToGene,GRangesList-method	Man page
TxToGene,data.frame-method	Man page
TxToGene,matrix-method	Man page
TxToGene-class	Man page
UcscGenes-class	Man page
UcscTranscripts-class	Man page
WormbaseGenes-class	Man page
WormbaseTranscripts-class	Man page
currentEnsemblGenomeBuild	Man page Source code
currentEnsemblVersion	Man page Source code
currentFlybaseVersion	Man page Source code
currentGencodeGenomeBuild	Man page Source code
currentGencodeVersion	Man page Source code
currentGenomeBuild	Man page
currentGenomeVersion	Man page
currentRefseqGenomeBuild	Man page Source code
currentRefseqVersion	Man page Source code
currentUcscGenomeBuild	Man page Source code
currentWormbaseVersion	Man page Source code
detectOrganism	Man page Source code
downloadEnsemblGenome	Man page Source code
downloadGencodeGenome	Man page Source code
downloadRefseqGenome	Man page Source code
downloadUcscGenome	Man page Source code
emptyRanges	Man page Source code
export	Man page
export,TxToGene,character-method	Man page
gencodeReleaseHistory	Man page Source code
importTxToGene	Man page Source code
makeEnsDbFromGff	Man page Source code
makeGRangesFromEnsDb	Man page Source code
makeGRangesFromEnsembl	Man page Source code
makeGRangesFromGff	Man page Source code
makeGeneToSymbol	Man page
makeGeneToSymbolFromEnsDb	Man page Source code
makeGeneToSymbolFromEnsembl	Man page Source code
makeGeneToSymbolFromGff	Man page Source code
makeProteinToGene	Man page
makeProteinToGeneFromEnsembl	Man page Source code
makeTxToGene	Man page
makeTxToGeneFromEnsDb	Man page Source code
makeTxToGeneFromEnsembl	Man page Source code
makeTxToGeneFromFasta	Man page Source code
makeTxToGeneFromGff	Man page Source code
mapEnsemblReleaseToUrl	Man page Source code
mapGencodeToEnsembl	Man page Source code
mapGeneNamesToEnsembl	Man page Source code
mapGeneNamesToHgnc	Man page Source code
mapGeneNamesToNcbi	Man page Source code
mapHumanOrthologs	Man page Source code
organism	Man page
organism,Annotated-method	Man page
organism,DFrame-method	Man page
organism,GRanges-method	Man page
organism,Matrix-method	Man page
organism,data.frame-method	Man page
organism,matrix-method	Man page
organism<-	Man page
organism<-,Annotated-method	Man page
params	Man page
show	Man page
show,EnsemblGenes-method	Man page
show,EnsemblTranscripts-method	Man page
show,FlybaseGenes-method	Man page
show,FlybaseTranscripts-method	Man page
show,GencodeGenes-method	Man page
show,GencodeTranscripts-method	Man page
show,RefseqGenes-method	Man page
show,RefseqTranscripts-method	Man page
show,UcscGenes-method	Man page
show,UcscTranscripts-method	Man page
show,WormbaseGenes-method	Man page
show,WormbaseTranscripts-method	Man page
stripGeneVersions	Man page
stripGeneVersions,Matrix-method	Man page
stripGeneVersions,character-method	Man page
stripGeneVersions,integer-method	Man page
stripGeneVersions,matrix-method	Man page
stripTranscriptVersions	Man page
stripTranscriptVersions,Matrix-method	Man page
stripTranscriptVersions,character-method	Man page
stripTranscriptVersions,integer-method	Man page
stripTranscriptVersions,matrix-method	Man page
summary	Man page
summary,GeneToSymbol-method	Man page
summary,TxToGene-method	Man page
updateObject	Man page
updateObject,EnsemblGenes-method	Man page
updateObject,EnsemblTranscripts-method	Man page
updateObject,GencodeGenes-method	Man page
updateObject,GencodeTranscripts-method	Man page