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Statistical Testing for ChIP-Seq data sets

Bioconductor version: Release (3.19)

This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).

Author: Gabriele Schweikert [cre, aut], David Kuo [aut]

Maintainer: Gabriele Schweikert <gschweik at>

Citation (from within R, enter citation("MMDiff2")):


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:

An Introduction to the MMDiff2 method PDF R Script
Reference Manual PDF


biocViews ChIPSeq, DifferentialPeakCalling, Sequencing, Software
Version 1.32.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License Artistic-2.0
Depends R (>= 3.5.0), Rsamtools, Biobase
Imports GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods
System Requirements
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Suggests MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9
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Follow Installation instructions to use this package in your R session.

Source Package MMDiff2_1.32.0.tar.gz
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macOS Binary (x86_64) MMDiff2_1.32.0.tgz
macOS Binary (arm64) MMDiff2_1.32.0.tgz
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Source Repository (Developer Access) git clone
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