# Generated by roxygen2: do not edit by hand

export("%>%")
export(PromoterAnnotation)
export(arrange)
export(as_tibble)
export(assays)
export(boxplotPromoters)
export(colData)
export(filter)
export(getAlternativePromoters)
export(group_by)
export(integrateProactiv)
export(loadDb)
export(mutate)
export(n)
export(plotHeatmap)
export(plotPCA)
export(preparePromoterAnnotation)
export(proActiv)
export(rowData)
export(rownames_to_column)
exportClasses(PromoterAnnotation)
exportMethods('intronRanges<-')
exportMethods('promoterCoordinates<-')
exportMethods('promoterIdMapping<-')
exportMethods(intronRanges)
exportMethods(promoterCoordinates)
exportMethods(promoterIdMapping)
importFrom(AnnotationDbi,loadDb)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpparam)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,counts)
importFrom(DESeq2,estimateSizeFactors)
importFrom(GenomeInfoDb,'seqlevelsStyle<-')
importFrom(GenomeInfoDb,keepStandardChromosomes)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicAlignments,readSTARJunctions)
importFrom(GenomicAlignments,readTopHatJunctions)
importFrom(GenomicAlignments,summarizeJunctions)
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,intronsByTranscript)
importFrom(GenomicFeatures,promoters)
importFrom(GenomicFeatures,transcripts)
importFrom(GenomicRanges,'strand<-')
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,width)
importFrom(IRanges,IRanges)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,'mcols<-')
importFrom(S4Vectors,'metadata<-')
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(SummarizedExperiment,'colData<-')
importFrom(SummarizedExperiment,'rowData<-')
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,`assays<-`)
importFrom(SummarizedExperiment,`rowData<-`)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,cbind)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(data.table,':=')
importFrom(data.table,.N)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,melt)
importFrom(dplyr,'%>%')
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,inner_join)
importFrom(dplyr,lead)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,slice_max)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_light)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(gplots,bluered)
importFrom(gplots,greenred)
importFrom(gplots,heatmap.2)
importFrom(gplots,redblue)
importFrom(gplots,redgreen)
importFrom(graphics,legend)
importFrom(methods,as)
importFrom(methods,new)
importFrom(methods,validObject)
importFrom(rlang,.data)
importFrom(scales,hue_pal)
importFrom(stats,complete.cases)
importFrom(stats,lm)
importFrom(stats,p.adjust)
importFrom(stats,prcomp)
importFrom(stats,quantile)
importFrom(stats,relevel)
importFrom(tibble,rownames_to_column)
importFrom(txdbmaker,makeTxDbFromGFF)
