ChIPbinner is published in BMC Bioinformatics: doi.org/10.1186/s12859-025-06103-6
Users can install the package using the two methods indicated below:
# install the 'remotes' package first and run the installation code below:
remotes::install_github("padilr1/ChIPbinner")
# download a '.tar.gz' file of ChIPbinner and run the installation code below:
install.packages("ChIPbinner_0.99.0.tar.gz",repos=NULL,type="source")
# the package vignette can be viewed using:
browseVignettes("ChIPbinner")
# if the vignette is still not visible, you can try forcing the installation of the package vignette directly:
remotes::install_github("padilr1/ChIPbinner",build_vignettes=TRUE)
ChIPbinner is an open-source R package designed to facilitate genome-wide analysis of broad histone modifications. This tool addresses limitations in existing peak-calling software, which often struggles to accurately detect diffuse and broad signals in ChIP-Seq, CUT&RUN/TAG or related datasets. ChIPbinner instead divides the genome into uniform bins, offering an unbiased, reference-agnostic method to identify and explore differential enrichment across genomic regions.
ChIPbinner provides users with functionalities for signal normalization and combining replicates, alongside visualization tools for exploratory analysis, including genic/intergenic scatterplots, principal component analysis and correlation plots. Finally, it allows users to identify clusters of similarly-behaving bins and statistically assess their overlap with specific classes of annotated regions.
ChIPbinner improves on previously published software by offering a clustering approach that is independent of differential binding and including additional features for downstream analysis.
Curated databases and complete published datasets for use with ChIPbinner can be found in this GitHub repository.
For a step-by-step tutorial on how to run ChIPbinner please see the workflow documentation