ChIPbinner: an R package for analyzing broad histone marks binned in uniform windows from ChIP-Seq or CUT&RUN/TAG data.

ABSTRACT:

Background

The decreasing costs of sequencing, along with the growing understanding of epigenetic mechanisms driving diseases, have led to the increased application of chromatin immunoprecipitation (ChIP), Cleavage Under Targets & Release Using Nuclease (CUT&RUN) and Cleavage Under Targets and Tagmentation (CUT&TAG) sequencing-which are designed to map DNA or chromatin-binding proteins to their genome targets-in biomedical research. Existing software tools, namely peak-callers, are available for analyzing data from these technologies, although they often struggle with diffuse and broad signals, such as those associated with broad histone post-translational modifications (PTMs).

Results

To address this limitation, we present ChIPbinner, an open-source R package tailored for r

SUBMITTER: Padilla R 

PROVIDER: S-EPMC11934474 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature