clusterComrades         clusterComrades
clusterGrangesList      clusterGrangesList
clusterGrangesList<-    clusterGrangesList<-
clusterNumbers          clusterNumbers
clusterTableFolded      clusterTableFolded
clusterTableList        clusterTableList
clusterTableList<-      clusterTableList<-
compareKnown            compareKnown
compareKnownStructures
                        compareKnownStructures
comradesDataSet-class   comradesDataSet
featureInfo             featureInfo
findBasePairsRNAcoFold2
                        findBasePairsRNAcoFold2
findBasePairsRNAfold    findBasePairsRNAfold
findBasePairsRNAfold2   findBasePairsRNAfold2
foldComrades            foldComrades
getAdjacancyMat         getAdjacancyMat
getClusterClusterShortRangeWhole
                        getClusterClusterShortRangeWhole
getData                 getData
getInteractions         getInteractions
getMatrices             getMatrices
getReverseInteractions
                        getReverseInteractions
group                   group
hybFiles                hybFiles
hybToGRanges            hybToGRanges
makeExampleComradesDataSet
                        makeExampleComradesDataSet
matrixList              matrixList
matrixList<-            matrixList
plotComparisonArc       plotComparisonArc
plotEnsemblePCA         plotEnsemblePCA
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
rnaSize                 rnaSize
rnas                    rnas
sampleChimeras          sampleChimeras
sampleNames             sampleNames
sampleTable             sampleTable
subsetHybList2          subsetHybList2
swapHybs                swapHybs
swapHybs2               swapHybs2
swapHybs3               swapHybs3
topInteracters          topInteracters
topInteractions         topInteractions
topTranscripts          topTranscripts
trimClusters            trimClusters
