API for acidgenomics/AcidGenomes
Acid Genomics Genome Annotations

Global functions
.addBroadClass Source code
.addGeneSynonyms Source code
.annotationHub Source code
.applyBroadClass Source code
.cacheIt Source code
.downloadEnsemblGFF Source code
.downloadEnsemblGTF Source code
.downloadEnsemblGenome Source code
.downloadEnsemblTranscriptome Source code
.downloadGencodeAnnotation Source code
.downloadGencodeGenome Source code
.downloadGencodeMetadata Source code
.downloadGencodeTranscriptome Source code
.downloadRefSeqAnnotation Source code
.downloadRefSeqGenome Source code
.downloadRefSeqMetadata Source code
.downloadRefSeqTranscriptome Source code
.downloadUCSCAnnotation Source code
.downloadUCSCGenome Source code
.downloadUCSCMetadata Source code
.downloadUCSCTranscriptome Source code
.downloadURLs Source code
.encodeMcols Source code
.ensemblValidity Source code
.flybaseValidity Source code
.gencodeValidity Source code
.getEnsDbAnnotationHubID Source code
.getEnsDbFromAnnotationHub Source code
.getEnsDbFromPackage Source code
.getEnsDbMetadata Source code
.getEnsembl2EntrezFromOrgDb Source code
.getFun Source code
.getRefSeqAssemblySummary Source code
.getRefSeqGenomeURL Source code
.getRefSeqSeqinfo Source code
.getSeqinfo Source code
.gffFormat Source code
.gffGenomeBuild Source code
.gffProvider Source code
.grangesValidity Source code
.includeGeneVersion Source code
.includeTxVersion Source code
.includeVersion Source code
.isSupportedGFF Source code
.locateRefSeqAssemblyReport Source code
.makeEnsembl2Entrez Source code
.makeGRanges Source code
.makeGRangesFromRtracklayer Source code
.mapGenomeBuildToUCSC Source code
.matchGRangesNamesColumn Source code
.matchNcbiTaxonomicGroup Source code
.md5 Source code
.refseqValidity 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
.simpleGenomeBuild Source code
.splitToCharacterList Source code
.standardizeMcols Source code
.ucscValidity Source code
.wormbaseValidity Source code
AcidGenomes Man page
AcidGenomes-package Man page
AcidGenomesTestsURL Man page
DataFrame Man page
Ensembl2Entrez Man page
Ensembl2Entrez,GRanges-method Man page
Ensembl2Entrez,character-method Man page
Ensembl2Entrez-class Man page
EnsemblGenes-class Man page
EnsemblTranscripts-class Man page
Entrez2Ensembl Man page
Entrez2Ensembl,integer-method Man page
Entrez2Ensembl-class Man page
EntrezGeneInfo Man page
EntrezGeneInfo-class Man page
FlyBaseGenes-class Man page
FlyBaseTranscripts-class Man page
GencodeGenes-class Man page
GencodeTranscripts-class Man page
Gene2Symbol Man page
Gene2Symbol,DataFrame-method Man page
Gene2Symbol,GRanges-method Man page
Gene2Symbol-class Man page
HGNC Man page
HGNC-class Man page
HGNC2Ensembl Man page
HGNC2Ensembl-class Man page
MGI2Ensembl Man page Source code
MGI2Ensembl-class Man page
Protein2Gene-class Man page
RefSeqGenes-class Man page
RefSeqTranscripts-class Man page
Tx2Gene Man page
Tx2Gene,DataFrame-method Man page
Tx2Gene,GRanges-method Man page
Tx2Gene,GRangesList-method Man page
Tx2Gene,data.frame-method Man page
Tx2Gene,matrix-method Man page
Tx2Gene-class Man page
UCSCGenes-class Man page
UCSCTranscripts-class Man page
WormBaseGenes-class Man page
WormBaseTranscripts-class Man page
annotable Man page Source code
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,Tx2Gene-method Man page
geneSynonyms Man page Source code
getEnsDb Man page Source code
getGFFDirectives Man page Source code
getGFFMetadata Man page Source code
importTx2Gene Man page Source code
makeEnsDbFromGFF Man page Source code
makeGRangesFromEnsDb Man page Source code
makeGRangesFromEnsembl Man page Source code
makeGRangesFromGFF Man page Source code
makeGRangesFromTxDb Man page Source code
makeGene2Symbol Man page
makeGene2SymbolFromEnsDb Man page Source code
makeGene2SymbolFromEnsembl Man page Source code
makeGene2SymbolFromGFF Man page Source code
makeProtein2Gene Man page
makeProtein2GeneFromEnsembl Man page Source code
makeTx2Gene Man page
makeTx2GeneFromEnsDb Man page Source code
makeTx2GeneFromEnsembl Man page Source code
makeTx2GeneFromFASTA Man page Source code
makeTx2GeneFromGFF Man page Source code
makeTxDbFromGFF Man page Source code
mapEnsemblReleaseToURL Man page Source code
mapHumanOrthologs Man page Source code
organism Man page
organism,Annotated-method Man page
organism,DataFrame-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
pasteURL Man page
reexports Man page
stripGeneVersions Man page
stripGeneVersions,Matrix-method Man page
stripGeneVersions,character-method Man page
stripGeneVersions,matrix-method Man page
stripTranscriptVersions Man page
stripTranscriptVersions,Matrix-method Man page
stripTranscriptVersions,character-method Man page
stripTranscriptVersions,matrix-method Man page
summary Man page
summary,Gene2Symbol-method Man page
summary,Tx2Gene-method Man page
acidgenomics/AcidGenomes documentation built on Sept. 16, 2021, 7:30 p.m.