recipe bioconductor-mmdiff2

Statistical Testing for ChIP-Seq data sets







biotools: mmdiff2, doi: 10.1038/nmeth.3252

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).

package bioconductor-mmdiff2

(downloads) docker_bioconductor-mmdiff2



depends bioconductor-biobase:


depends bioconductor-biostrings:


depends bioconductor-bsgenome:


depends bioconductor-genomicranges:


depends bioconductor-rsamtools:


depends bioconductor-s4vectors:


depends r-base:


depends r-ggplot2:

depends r-locfit:

depends r-rcolorbrewer:

depends r-shiny:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-mmdiff2

and update with::

   mamba update bioconductor-mmdiff2

To create a new environment, run:

mamba create --name myenvname bioconductor-mmdiff2

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-mmdiff2/tags`_ for valid values for ``<tag>``)

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