| 'intronRanges<-'-method | S4 class for promoter annotation data for a specific annotation version | 
| 'promoterCoordinates<-'-method | S4 class for promoter annotation data for a specific annotation version | 
| 'promoterIdMapping<-'-method | S4 class for promoter annotation data for a specific annotation version | 
| boxplotPromoters | Visualizes promoter activity and gene expression with boxplots | 
| calculateJunctionReadCounts | Calculate the total number of junction reads overlapping with the introns of each promoter for the input junction file | 
| calculatePromoterReadCounts | Calculate the promoter read counts using junction read counts approach for all the input junction files | 
| getAbsolutePromoterActivity | Prepare the absolute promoter activity table including the promoter and gene ids | 
| getAlternativePromoters | Identifies alternative promoters. | 
| getGeneExpression | Prepare the gene expression table including the gene ids | 
| getRelativePromoterActivity | Prepare the relative promoter activity table including the promoter and gene ids | 
| integrateProactiv | Integrate multiple proActiv runs | 
| intronRanges | S4 class for promoter annotation data for a specific annotation version | 
| intronRanges-method | S4 class for promoter annotation data for a specific annotation version | 
| intronRanges<- | S4 class for promoter annotation data for a specific annotation version | 
| intronRanges<--method | S4 class for promoter annotation data for a specific annotation version | 
| normalizePromoterReadCounts | Normalize promoter read counts using DESeq2 | 
| plotHeatmap | Visualizes heatmap of features for samples | 
| plotPCA | Performs principal component analysis | 
| preparePromoterAnnotation | Prepares promoter annotation from a gtf or txdb | 
| proActiv | Estimates promoter counts and activity in a single command | 
| PromoterAnnotation | S4 class for promoter annotation data for a specific annotation version | 
| PromoterAnnotation-class | S4 class for promoter annotation data for a specific annotation version | 
| promoterAnnotation.gencode.v34.subset | Promoter annotation for Gencode.v34 (subset) | 
| promoterCoordinates | S4 class for promoter annotation data for a specific annotation version | 
| promoterCoordinates-method | S4 class for promoter annotation data for a specific annotation version | 
| promoterCoordinates<- | S4 class for promoter annotation data for a specific annotation version | 
| promoterCoordinates<--method | S4 class for promoter annotation data for a specific annotation version | 
| promoterIdMapping | S4 class for promoter annotation data for a specific annotation version | 
| promoterIdMapping-method | S4 class for promoter annotation data for a specific annotation version | 
| promoterIdMapping<- | S4 class for promoter annotation data for a specific annotation version | 
| promoterIdMapping<--method | S4 class for promoter annotation data for a specific annotation version |