clusterGrangesList	clusterGrangesList
clusterGrangesList,rnaCrosslinkDataSet-method	clusterGrangesList
clusterGrangesList<-	clusterGrangesList_set
clusterGrangesList<-,rnaCrosslinkDataSet-method	clusterGrangesList_set
clusterNumbers	clusterNumbers
clusterNumbers,rnaCrosslinkDataSet-method	clusterNumbers
clusterrnaCrosslink	clusterrnaCrosslink
clusterrnaCrosslink,rnaCrosslinkDataSet-method	clusterrnaCrosslink
clusterTableFolded	clusterTableFolded
clusterTableFolded,rnaCrosslinkDataSet-method	clusterTableFolded
clusterTableList	clusterTableList
clusterTableList,rnaCrosslinkDataSet-method	clusterTableList
clusterTableList<-	clusterTableList_set
clusterTableList<-,rnaCrosslinkDataSet-method	clusterTableList_set
compareKnown	compareKnown
compareKnown,rnaCrosslinkDataSet-method	compareKnown
compareKnownStructures	compareKnownStructures
compareKnownStructures,rnaCrosslinkDataSet-method	compareKnownStructures
featureInfo	featureInfo
featureInfo,rnaCrosslinkDataSet-method	featureInfo
findBasePairsRNAcoFold2	findBasePairsRNAcoFold2
findBasePairsRNAfold	findBasePairsRNAfold
findBasePairsRNAfold2	findBasePairsRNAfold2
foldrnaCrosslink	foldrnaCrosslink
foldrnaCrosslink,rnaCrosslinkDataSet-method	foldrnaCrosslink
getAdjacancyMat	getAdjacancyMat
getClusterClusterShortRangeWhole	getClusterClusterShortRangeWhole
getData	getData
getData,rnaCrosslinkDataSet-method	getData
getInteractions	getInteractions
getInteractions,rnaCrosslinkDataSet-method	getInteractions
getMatrices	getMatrices
getReverseInteractions	getReverseInteractions
getReverseInteractions,rnaCrosslinkDataSet-method	getReverseInteractions
group	group
group,rnaCrosslinkDataSet-method	group
InputFiles	InputFiles
InputFiles,rnaCrosslinkDataSet-method	InputFiles
InputToGRanges	InputToGRanges
makeExamplernaCrosslinkDataSet	makeExamplernaCrosslinkDataSet
matrixList	matrixList
matrixList,rnaCrosslinkDataSet-method	matrixList
matrixList<-	matrixList_set
matrixList<-,rnaCrosslinkDataSet-method	matrixList_set
plotClusterAgreement	plotClusterAgreement
plotClusterAgreement,rnaCrosslinkDataSet-method	plotClusterAgreement
plotClusterAgreementHeat	plotClusterAgreementHeat
plotClusterAgreementHeat,rnaCrosslinkDataSet-method	plotClusterAgreementHeat
plotCombinedMatrix	plotCombinedMatrix
plotCombinedMatrix,rnaCrosslinkDataSet-method	plotCombinedMatrix
plotComparisonArc	plotComparisonArc
plotComparisonArc,rnaCrosslinkDataSet-method	plotComparisonArc
plotEnsemblePCA	plotEnsemblePCA
plotEnsemblePCA,rnaCrosslinkDataSet-method	plotEnsemblePCA
plotInteractions	plotInteractions
plotInteractions,rnaCrosslinkDataSet-method	plotInteractions
plotInteractionsAverage	plotInteractionsAverage
plotInteractionsAverage,rnaCrosslinkDataSet-method	plotInteractionsAverage
plotMatrices	plotMatrices
plotMatrices,rnaCrosslinkDataSet-method	plotMatrices
plotMatricesAverage	plotMatricesAverage
plotMatricesAverage,rnaCrosslinkDataSet-method	plotMatricesAverage
plotStructure	plotStructure
plotStructure,rnaCrosslinkDataSet-method	plotStructure
printClustersFast	printClustersFast
readNumbers	readNumbers
readNumbers,rnaCrosslinkDataSet-method	readNumbers
rnaCrosslinkDataSet	rnaCrosslinkDataSet
rnaCrosslinkDataSet-class	rnaCrosslinkDataSet
rnaCrosslinkOO	rnaCrosslinkOO
rnaCrosslinkQC	rnaCrosslinkQC
rnas	rnas
rnas,rnaCrosslinkDataSet-method	rnas
rnaSize	rnaSize
rnaSize,rnaCrosslinkDataSet-method	rnaSize
sampleChimeras	sampleChimeras
sampleNames	sampleNames
sampleNames,rnaCrosslinkDataSet-method	sampleNames
sampleTable	sampleTable
sampleTable,rnaCrosslinkDataSet-method	sampleTable
subsetInputList2	subsetInputList2
swapInputs	swapInputs
swapInputs2	swapInputs2
swapInputs3	swapInputs3
topInteracters	topInteracters
topInteracters,rnaCrosslinkDataSet-method	topInteracters
topInteractions	topInteractions
topInteractions,rnaCrosslinkDataSet-method	topInteractions
topTranscripts	topTranscripts
topTranscripts,rnaCrosslinkDataSet-method	topTranscripts
trimClusters	trimClusters
trimClusters,rnaCrosslinkDataSet-method	trimClusters
