InputFiles              InputFiles
InputToGRanges          InputToGRanges
clusterGrangesList      clusterGrangesList
clusterGrangesList<-    clusterGrangesList<-
clusterNumbers          clusterNumbers
clusterTableFolded      clusterTableFolded
clusterTableList        clusterTableList
clusterTableList<-      clusterTableList<-
clusterrnaCrosslink     clusterrnaCrosslink
compareKnown            compareKnown
compareKnownStructures
                        compareKnownStructures
featureInfo             featureInfo
findBasePairsRNAcoFold2
                        findBasePairsRNAcoFold2
findBasePairsRNAfold    findBasePairsRNAfold
findBasePairsRNAfold2   findBasePairsRNAfold2
foldrnaCrosslink        foldrnaCrosslink
getAdjacancyMat         getAdjacancyMat
getClusterClusterShortRangeWhole
                        getClusterClusterShortRangeWhole
getData                 getData
getInteractions         getInteractions
getMatrices             getMatrices
getReverseInteractions
                        getReverseInteractions
group                   group
makeExamplernaCrosslinkDataSet
                        makeExamplernaCrosslinkDataSet
matrixList              matrixList
matrixList<-            matrixList
plotClusterAgreement    Plot a heatmap that plots the agreements
                        between replicates after clusterrnaCrosslink
                        has been performed
plotClusterAgreementHeat
                        Plot a heatmap that plots the agreements
                        between replicates after clusterrnaCrosslink
                        has been performed
plotCombinedMatrix      Plots a contact map of two chosen samples for
                        chosen stages in the analysis, with each chosen
                        sample on separate halves of the contact map
plotComparisonArc       plotComparisonArc
plotEnsemblePCA         plotEnsemblePCA
plotInteractions        Plots a contact map of interactions of each
                        sample of an RNA (interactor) on the RNA of
                        interest
plotInteractionsAverage
                        Plots a contact map of interactions of all
                        samples of an RNA (interactor) on the RNA of
                        interest
plotMatrices            Plots a number of contact maps to file of each
                        sample for a stage in the analysis
plotMatricesAverage     plotMatricesAverage
plotStructure           plotStructure
printClustersFast       printClustersFast
readNumbers             readNumbers
rnaCrosslinkDataSet-class
                        rnaCrosslinkDataSet
rnaCrosslinkQC          rnaCrosslinkQC
rnaSize                 rnaSize
rnas                    rnas
sampleChimeras          sampleChimeras
sampleNames             sampleNames
sampleTable             sampleTable
subsetInputList2        subsetInputList2
swapInputs              swapInputs
swapInputs2             swapInputs2
swapInputs3             swapInputs3
topInteracters          topInteracters
topInteractions         topInteractions
topTranscripts          topTranscripts
trimClusters            trimClusters
