'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 |