# Generated by roxygen2: do not edit by hand

export("clusterGrangesList<-")
export("clusterTableList<-")
export("matrixList<-")
export(InputFiles)
export(clusterGrangesList)
export(clusterNumbers)
export(clusterTableFolded)
export(clusterTableList)
export(clusterrnaCrosslink)
export(compareKnown)
export(compareKnownStructures)
export(featureInfo)
export(foldrnaCrosslink)
export(getData)
export(getInteractions)
export(getReverseInteractions)
export(group)
export(makeExamplernaCrosslinkDataSet)
export(matrixList)
export(plotClusterAgreement)
export(plotClusterAgreementHeat)
export(plotCombinedMatrix)
export(plotComparisonArc)
export(plotEnsemblePCA)
export(plotInteractions)
export(plotInteractionsAverage)
export(plotMatrices)
export(plotMatricesAverage)
export(plotStructure)
export(readNumbers)
export(rnaCrosslinkDataSet)
export(rnaCrosslinkQC)
export(rnaSize)
export(rnas)
export(sampleNames)
export(sampleTable)
export(topInteracters)
export(topInteractions)
export(topTranscripts)
export(trimClusters)
exportClasses(rnaCrosslinkDataSet)
import("MASS", except = area)
import(GenomicRanges)
import(R4RNA)
import(RColorBrewer)
import(RRNA)
import(TopDom)
import(foreach)
import(ggplot2)
import(ggrepel)
import(heatmap3)
import(mixtools)
import(patchwork)
import(reshape2)
import(tidyverse)
import(utils)
importFrom(ClassDiscovery,aspectHeatmap)
importFrom(IRanges,IRanges)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(doParallel,registerDoParallel)
importFrom(doParallel,stopImplicitCluster)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(igraph,cluster_walktrap)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,membership)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(parallel,makeCluster)
importFrom(parallel,stopCluster)
importFrom(seqinr,read.fasta)
importFrom(stats,aggregate)
importFrom(stats,complete.cases)
importFrom(stats,median)
importFrom(stats,prcomp)
importFrom(stats,reorder)
