DOI: 10.18129/B9.bioc.MMDiff2  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see MMDiff2.

Statistical Testing for ChIP-Seq data sets

Bioconductor version: 3.16

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 "4.2") and enter:

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


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


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


biocViews ChIPSeq, DifferentialPeakCalling, Sequencing, Software
Version 1.26.0
In Bioconductor since BioC 3.3 (R-3.3) (7 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
Suggests MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9
Depends On Me
Imports Me
Suggests Me MMDiffBamSubset
Links To Me
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