# Generated by roxygen2: do not edit by hand

export(.valid.Assays)
export(CircosTargets)
export(PCIT)
export(RIF)
export(RIFPlot)
export(SmearPlot)
export(bivar.awk)
export(clustCoef)
export(clustCoefPercentage)
export(densityPlot)
export(diffusion)
export(enrichPlot)
export(expDiff)
export(getEnrich)
export(getGroupGO)
export(heatPlot)
export(histPlot)
export(netConditionsPlot)
export(netGOTFPlot)
export(normExp)
export(pcitC)
export(runAnalysis)
export(tolerance)
exportClasses(CeTF)
exportMethods(InputData)
exportMethods(NetworkData)
exportMethods(OutputData)
exportMethods(getDE)
exportMethods(getData)
import(Rcpp)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,Legend)
importFrom(ComplexHeatmap,anno_barplot)
importFrom(ComplexHeatmap,anno_simple)
importFrom(ComplexHeatmap,anno_text)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,max_text_width)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,results)
importFrom(GGally,ggnet2)
importFrom(GenomicTools,gtfToBed)
importFrom(GenomicTools.fileHandler,importGTF)
importFrom(Matrix,Matrix)
importFrom(RCy3,commandsPOST)
importFrom(RCy3,createIgraphFromNetwork)
importFrom(RCy3,createNetworkFromIgraph)
importFrom(RCy3,createSubnetwork)
importFrom(RCy3,cytoscapePing)
importFrom(RCy3,selectNodes)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,setValidity2)
importFrom(SummarizedExperiment,Assays)
importFrom(SummarizedExperiment,colData)
importFrom(circlize,CELL_META)
importFrom(circlize,circos.clear)
importFrom(circlize,circos.initialize)
importFrom(circlize,circos.link)
importFrom(circlize,circos.par)
importFrom(circlize,circos.rect)
importFrom(circlize,circos.text)
importFrom(circlize,circos.track)
importFrom(circlize,colorRamp2)
importFrom(circlize,highlight.chromosome)
importFrom(circlize,rand_color)
importFrom(clusterProfiler,enrichGO)
importFrom(clusterProfiler,groupGO)
importFrom(dplyr,'%>%')
importFrom(dplyr,across)
importFrom(dplyr,everything)
importFrom(dplyr,mutate)
importFrom(ggnetwork,geom_edges)
importFrom(ggnetwork,geom_nodes)
importFrom(ggnetwork,geom_nodetext)
importFrom(ggnetwork,ggnetwork)
importFrom(ggnetwork,theme_facet)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_equal)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,coord_polar)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,fortify)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_step)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_brewer)
importFrom(ggplot2,scale_color_gradient)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_continuous)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_size_continuous)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(ggpubr,ggarrange)
importFrom(ggrepel,geom_label_repel)
importFrom(graphics,hist)
importFrom(graphics,layout)
importFrom(graphics,title)
importFrom(grid,gpar)
importFrom(grid,unit)
importFrom(igraph,as_long_data_frame)
importFrom(igraph,graph_from_data_frame)
importFrom(methods,is)
importFrom(methods,new)
importFrom(network,'%v%')
importFrom(network,'%v%<-')
importFrom(network,network)
importFrom(network,network.vertex.names)
importFrom(network,set.edge.attribute)
importFrom(stats,cor)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,relevel)
importFrom(stats,sd)
importFrom(utils,head)
importFrom(utils,packageDescription)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(utils,txtProgressBar)
useDynLib(CeTF)
