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A Bioconductor Workflow to Detect Differential Binding in ChIP-seq Data

Bioconductor version: Release (3.19)

Describes a computational workflow for performing a DB analysis with sliding windows. The aim is to facilitate the practical implementation of window-based DB analyses by providing detailed code and expected output. The workflow described here applies to any ChIP-seq experiment with multiple experimental conditions and multiple biological samples in one or more of the conditions. It detects and summarizes DB regions between conditions in a de novo manner, i.e., without making any prior assumptions about the location or width of bound regions. Detected regions are then annotated according to their proximity to genes.

Author: Aaron Lun [aut, cre], Gordon Smyth [aut]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at>

Citation (from within R, enter citation("chipseqDB")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

1. Introduction HTML
2. Differential enrichment of H3K9ac in B cells HTML
3. Differential binding of CBP in fibroblasts HTML R Script
4. Differential enrichment of H3K27me3 in lung epithelium HTML


biocViews EpigeneticsWorkflow, ImmunoOncologyWorkflow, Workflow
Version 1.28.0
License Artistic-2.0
System Requirements
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Suggests chipseqDBData, BiocStyle, BiocFileCache, ChIPpeakAnno, Gviz, Rsamtools, TxDb.Mmusculus.UCSC.mm10.knownGene, csaw, edgeR, knitr,, rtracklayer, rmarkdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package chipseqDB_1.28.0.tar.gz
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