refGenome-package	refGenome-package
+,geneList,geneList-method	geneList-class
+,geneModel,geneModel-method	geneModel-class
addEnsembl	ucscGenome-class
addEnsembl,ucscGenome-method	ucscGenome-class
addEnsembl-methods	ucscGenome-class
addIsCoding	addIsCoding
addIsCoding,ensemblJunctions-method	addIsCoding
addIsCoding-methods	addIsCoding
addIsoforms	ucscGenome-class
addIsoforms,ucscGenome-method	ucscGenome-class
addIsoforms-methods	ucscGenome-class
addXref	ucscGenome-class
addXref,ucscGenome-method	ucscGenome-class
addXref-methods	ucscGenome-class
basedir	refGenome-class
basedir,refGenome-method	refGenome-class
basedir-methods	refGenome-class
basedir<-	refGenome-class
basedir<-,refGenome-method	refGenome-class
basedir<--methods	refGenome-class
ensemblExons	refExons-class
ensemblExons-class	refExons-class
ensemblGenome	ensemblGenome-class
ensemblGenome-class	ensemblGenome-class
ensemblJunctions	refJunctions-class
ensemblJunctions-class	refJunctions-class
ensPrimAssembly	refGenome-class
extractByGeneId	extractByGeneID
extractByGeneId,refGenome,character-method	extractByGeneID
extractByGeneId,refJunctions,character-method	extractByGeneID
extractByGeneId-methods	extractByGeneID
extractByGeneName	extractByGeneName
extractByGeneName,refGenome,character-method	extractByGeneName
extractByGeneName,refJunctions,character-method	extractByGeneName
extractByGeneName-methods	extractByGeneName
extractFeature	refGenome-class
extractFeature,refGenome,character-method	refGenome-class
extractFeature-methods	refGenome-class
extractPaGenes	ensemblGenome-class
extractPaGenes,ensemblGenome-method	ensemblGenome-class
extractPaGenes-methods	ensemblGenome-class
extractSeqids	refGenome-class
extractSeqids,refGenome-method	refGenome-class
extractSeqids-methods	refGenome-class
extractTranscript	refGenome-class
extractTranscript,refGenome,character-method	refGenome-class
extractTranscript,ucscGenome-method	ucscGenome-class
extractTranscript-methods	refGenome-class
geneId<-	geneModel-class
geneId<-,geneModel,character-method	geneModel-class
geneId<-,geneModel,factor-method	geneModel-class
geneId<--methods	geneModel-class
geneList	geneList-class
geneList,ensemblGenome,character-method	geneList-class
geneList,ensemblGenome,factor-method	geneList-class
geneList,ucscGenome,character-method	geneList-class
geneList,ucscGenome,factor-method	geneList-class
geneList-class	geneList-class
geneList-methods	geneList-class
geneModel	geneModel-class
geneModel,ensemblGenome,character-method	geneModel-class
geneModel,ucscGenome,character-method	geneModel-class
geneModel-class	geneModel-class
geneModel-methods	geneModel-class
geneName<-	geneModel-class
geneName<-,geneModel,character-method	geneModel-class
geneName<-,geneModel,factor-method	geneModel-class
geneName<--methods	geneModel-class
getCdsData	transcriptModel-class
getCdsData,transcriptModel-method	transcriptModel-class
getCdsData-methods	transcriptModel-class
getExonData	transcriptModel-class
getExonData,transcriptModel-method	transcriptModel-class
getExonData-methods	transcriptModel-class
getGeneId	getGeneId
getGeneId,ensemblGenome,character-method	getGeneId
getGeneId,ensemblGenome,factor-method	getGeneId
getGeneId-methods	getGeneId
getGenePositions	getGenePositions
getGenePositions,ensemblGenome,character-method	getGenePositions
getGenePositions,ensemblGenome,missing-method	getGenePositions
getGenePositions,refJunctions,ANY-method	getGenePositions
getGenePositions,ucscGenome,ANY-method	getGenePositions
getGenePositions,ucscGenome-method	ucscGenome-class
getGenePositions-methods	getGenePositions
getGeneTable	ensemblGenome-class
getGeneTable,ensemblGenome-method	ensemblGenome-class
getGeneTable,ucscGenome-method	ucscGenome-class
getGeneTable-methods	ensemblGenome-class
getGtf	refGenome-class
getGtf,refGenome-method	refGenome-class
getGtf-methods	refGenome-class
getSpliceTable	refJunctions-class
getSpliceTable,refGenome-method	refJunctions-class
getSpliceTable-methods	refJunctions-class
getTranscript	transcriptModel-class
getTranscript,geneModel,character-method	transcriptModel-class
getTranscript,geneModel,numeric-method	transcriptModel-class
getTranscript-methods	transcriptModel-class
getXref	ucscGenome-class
getXref,ucscGenome-method	ucscGenome-class
getXref-methods	ucscGenome-class
initialize,geneList-method	geneList-class
initialize,geneModel-method	geneModel-class
initialize,refGenome-method	refGenome-class
initialize,transcriptModel-method	transcriptModel-class
length,geneList-method	geneList-class
loadGenome	saveGenome
loadGenomeDb	writeDB
names,geneList-method	geneList-class
names<-,geneList,character-method	geneList-class
names<-,geneList,numeric-method	geneList-class
overlap	overlap
overlapJuncs	overlapJuncs
plot.geneModel	geneModel-class
plot.transcriptModel	transcriptModel-class
plotUbs	unifyRanges
plotUbs,unifiedExons-method	unifyRanges
plotUbs-methods	unifyRanges
read.gtf	readGtf
read.gtf,refGenome-method	readGtf
read.gtf-methods	readGtf
refExons	refExons-class
refExons,refGenome-method	refExons-class
refExons-class	refExons-class
refExons-methods	refExons-class
refGenome-class	refGenome-class
refJunctions	refJunctions-class
refJunctions-class	refJunctions-class
saveGenome	saveGenome
saveGenome,refGenome-method	saveGenome
saveGenome-methods	saveGenome
setGtf	refGenome-class
setGtf,refGenome-method	refGenome-class
setGtf-methods	refGenome-class
show,geneList-method	geneList-class
tableFeatures	ensemblGenome-class
tableFeatures,ensemblGenome-method	ensemblGenome-class
tableFeatures,ucscGenome-method	ucscGenome-class
tableFeatures-methods	ensemblGenome-class
tableSeqids	refGenome-class
tableSeqids,refGenome-method	refGenome-class
tableSeqids-methods	refGenome-class
tableTranscript.id	ensemblGenome-class
tableTranscript.id,ensemblGenome-method	ensemblGenome-class
tableTranscript.id,ucscGenome-method	ucscGenome-class
tableTranscript.id-methods	ensemblGenome-class
tableTranscript.name	ensemblGenome-class
tableTranscript.name,ensemblGenome-method	ensemblGenome-class
tableTranscript.name-methods	ensemblGenome-class
transcriptModel-class	transcriptModel-class
ucPrimAssembly	refGenome-class
ucscExons	refExons-class
ucscExons-class	refExons-class
ucscGenome	ucscGenome-class
ucscGenome-class	ucscGenome-class
ucscJunctions	refJunctions-class
ucscJunctions-class	refJunctions-class
unifiedExons-class	refExons-class
unifyJuncs	unifyJuncs
unifyJuncs,refJunctions-method	unifyJuncs
unifyJuncs-methods	unifyJuncs
unifyRanges	unifyRanges
unifyRanges,refExons-method	unifyRanges
unifyRanges-methods	unifyRanges
writeDB	writeDB
writeDB,refGenome-method	writeDB
writeDB-methods	writeDB
[,geneList,ANY,ANY,ANY-method	geneList-class
