Estimate Promoter Activity from RNA-Seq data


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Documentation for package ‘proActiv’ version 1.6.0

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'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