comradesOO-package	comradesOO
clusterComrades	clusterComrades
clusterComrades,comradesDataSet-method	clusterComrades
clusterGrangesList	clusterGrangesList
clusterGrangesList,comradesDataSet-method	clusterGrangesList
clusterGrangesList<-	clusterGrangesList_set
clusterGrangesList<-,comradesDataSet-method	clusterGrangesList_set
clusterNumbers	clusterNumbers
clusterNumbers,comradesDataSet-method	clusterNumbers
clusterTableFolded	clusterTableFolded
clusterTableFolded,comradesDataSet-method	clusterTableFolded
clusterTableList	clusterTableList
clusterTableList,comradesDataSet-method	clusterTableList
clusterTableList<-	clusterTableList_set
clusterTableList<-,comradesDataSet-method	clusterTableList_set
compareKnown	compareKnown
compareKnown,comradesDataSet-method	compareKnown
compareKnownStructures	compareKnownStructures
compareKnownStructures,comradesDataSet-method	compareKnownStructures
comradesDataSet	comradesDataSet
comradesDataSet-class	comradesDataSet
comradesOO	comradesOO
featureInfo	featureInfo
featureInfo,comradesDataSet-method	featureInfo
findBasePairsRNAcoFold2	findBasePairsRNAcoFold2
findBasePairsRNAfold	findBasePairsRNAfold
findBasePairsRNAfold2	findBasePairsRNAfold2
foldComrades	foldComrades
foldComrades,comradesDataSet-method	foldComrades
getAdjacancyMat	getAdjacancyMat
getClusterClusterShortRangeWhole	getClusterClusterShortRangeWhole
getData	getData
getData,comradesDataSet-method	getData
getInteractions	getInteractions
getInteractions,comradesDataSet-method	getInteractions
getMatrices	getMatrices
getReverseInteractions	getReverseInteractions
getReverseInteractions,comradesDataSet-method	getReverseInteractions
group	group
group,comradesDataSet-method	group
hybFiles	hybFiles
hybFiles,comradesDataSet-method	hybFiles
hybToGRanges	hybToGRanges
makeExampleComradesDataSet	makeExampleComradesDataSet
matrixList	matrixList
matrixList,comradesDataSet-method	matrixList
matrixList<-	matrixList_set
matrixList<-,comradesDataSet-method	matrixList_set
plotComparisonArc	plotComparisonArc
plotComparisonArc,comradesDataSet-method	plotComparisonArc
plotEnsemblePCA	plotEnsemblePCA
plotEnsemblePCA,comradesDataSet-method	plotEnsemblePCA
plotMatrices	plotMatrices
plotMatrices,comradesDataSet-method	plotMatrices
plotMatricesAverage	plotMatricesAverage
plotMatricesAverage,comradesDataSet-method	plotMatricesAverage
plotStructure	plotStructure
plotStructure,comradesDataSet-method	plotStructure
printClustersFast	printClustersFast
readNumbers	readNumbers
readNumbers,comradesDataSet-method	readNumbers
rnas	rnas
rnas,comradesDataSet-method	rnas
rnaSize	rnaSize
rnaSize,comradesDataSet-method	rnaSize
sampleChimeras	sampleChimeras
sampleNames	sampleNames
sampleNames,comradesDataSet-method	sampleNames
sampleTable	sampleTable
sampleTable,comradesDataSet-method	sampleTable
subsetHybList2	subsetHybList2
swapHybs	swapHybs
swapHybs2	swapHybs2
swapHybs3	swapHybs3
topInteracters	topInteracters
topInteracters,comradesDataSet-method	topInteracters
topInteractions	topInteractions
topInteractions,comradesDataSet-method	topInteractions
topTranscripts	topTranscripts
topTranscripts,comradesDataSet-method	topTranscripts
trimClusters	trimClusters
trimClusters,comradesDataSet-method	trimClusters
