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Differential Binding Analysis of ChIP-Seq Peak Data

Bioconductor version: Release (3.19)

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Author: Rory Stark [aut, cre], Gord Brown [aut]

Maintainer: Rory Stark <bioconductor at>

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


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:

DiffBind: Differential binding analysis of ChIP-Seq peak data PDF R Script
Reference Manual PDF


biocViews ATACSeq, BiomedicalInformatics, CellBiology, ChIPSeq, DNaseSeq, DifferentialMethylation, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneRegulation, HistoneModification, MethylSeq, MultipleComparison, Normalization, PeakDetection, RIPSeq, ReportWriting, Sequencing, Software
Version 3.14.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License Artistic-2.0
Depends R (>= 4.0), GenomicRanges, SummarizedExperiment
Imports RColorBrewer, amap, gplots, grDevices, limma, GenomicAlignments, locfit, stats, utils, IRanges, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools(>= 2.13.1), DESeq2, methods, graphics, ggrepel, apeglm, ashr, GreyListChIP
System Requirements GNU make
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Suggests BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid
Linking To Rhtslib(>= 1.99.1), Rcpp
Depends On Me ChIPQC, vulcan
Imports Me
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package DiffBind_3.14.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) DiffBind_3.14.0.tgz
macOS Binary (arm64) DiffBind_3.14.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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