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

## 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