# Generated by roxygen2: do not edit by hand

export(BetaViolinPlot)
export(ChiViolinPlot)
export(betaTbl)
export(chiTbl)
export(combinedCellsData)
export(counts)
export(estimateTranscriptionRates)
export(finalPositionMatrix)
export(geneBodyRegions)
export(getAvailableTimePoints)
export(getCombinedCellsDataAtTime)
export(getPositionMatrixAtTime)
export(likelihoodRatioTest)
export(omegaScale)
export(parameters)
export(pauseRegions)
export(pauseSites)
export(plotBetaVsChi)
export(plotChiDistrib)
export(plotCombinedCells)
export(plotExpectedVsActualPauseSiteCounts)
export(plotLfcMa)
export(plotMeanPauseDistrib)
export(plotPauseSiteContourMap)
export(plotPauseSiteContourMapTwoConditions)
export(plotPauseSites)
export(plotPolymerasePCA)
export(plotPositionHeatmap)
export(positionMatrices)
export(rates)
export(readCounts)
export(sampleReadCounts)
export(simpol)
export(simulatePolymerase)
export(siteProbabilities)
export(spikeInFile)
export(stericHindrance)
export(transcriptionRates1)
export(transcriptionRates2)
exportClasses(ExperimentTranscriptionRates)
exportClasses(SimulatePolymerase)
exportClasses(SimulationTranscriptionRates)
exportClasses(TranscriptionRates)
exportClasses(TranscriptionRatesLRT)
exportMethods(estimateTranscriptionRates)
exportMethods(rates)
exportMethods(show)
exportMethods(stericHindrance)
importClassesFrom(GenomicRanges,CompressedGRangesList)
importClassesFrom(GenomicRanges,GRanges)
importClassesFrom(data.table,data.table)
importClassesFrom(tibble,tbl_df)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicRanges,"strand<-")
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,coverage)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,promoters)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,width)
importFrom(IRanges,IRanges)
importFrom(MASS,kde2d)
importFrom(Rcpp,evalCpp)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,splitAsList)
importFrom(dplyr,"%>%")
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_density_2d)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_gradient)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylim)
importFrom(grDevices,nclass.Sturges)
importFrom(methods,"slot<-")
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(methods,validObject)
importFrom(plyranges,group_by)
importFrom(plyranges,group_by_overlaps)
importFrom(plyranges,summarise)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map_chr)
importFrom(purrr,map_dbl)
importFrom(purrr,pmap)
importFrom(rlang,.data)
importFrom(rlang,sym)
importFrom(rtracklayer,import.bw)
importFrom(stats,cor)
importFrom(stats,density)
importFrom(stats,dnorm)
importFrom(stats,optim)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,prcomp)
importFrom(stats,rnorm)
importFrom(stats,rpois)
importFrom(stats,sd)
importFrom(stats,uniroot)
importFrom(stats,var)
importFrom(tibble,as_tibble)
importFrom(tibble,tibble)
importFrom(utils,head)
importFrom(utils,read.csv)
useDynLib(STADyUM, .registration = TRUE)
