An R package to predict condition-specific enhancers from ChIP-seq data

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Documentation for package ‘crupR’ version 1.0.0

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

Help Pages

crupR-package	crupR: Condition-specific Regulatory Units Prediction
crupR	crupR: Condition-specific Regulatory Units Prediction
getDynamics	Clusters the active enhancer into condition-specific groups
getEnhancers	Predicts the occurence of enhancers using the normalized HMs counts.
getSE	Find enhancer peaks and super enhancers
getTargets	Find the target genes of the regulatory, condition-specific clusters
normalize	Normalization of ChIP-seq counts by input
plotSummary	plots boxplots of the max. enhancer prediction values of the enhancers in the condition-specific clusters
saveFiles	Function to save the different output objects of each step