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Package with a quality control pipeline for ChIP-exo/nexus data.

ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.

Bayesian hidden Ising models are implemented to identify IP-enriched genomic regions from ChIP-seq data. They can be used to analyze ChIP-seq data with and without controls and replicates.