Estimate Promoter Activity from RNA-Seq data

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Documentation for package ‘proActiv’ version 1.12.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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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