recipe bioconductor-cohcap

CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data







biotools: cohcap

COHCAP (pronounced "co-cap") provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options. Discussion Group:

package bioconductor-cohcap

(downloads) docker_bioconductor-cohcap



depends bioconductor-cohcapanno:


depends bioconductor-cohcapanno:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends perl:

>=5.32.1,<5.33.0a0 *_perl5

depends perl:


depends r-base:


depends r-bh:

depends r-gplots:

depends r-rcolorbrewer:

depends r-rcpp:

depends r-rcpparmadillo:

depends r-writexls:



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-cohcap

and update with::

   mamba update bioconductor-cohcap

To create a new environment, run:

mamba create --name myenvname bioconductor-cohcap

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-cohcap/tags`_ for valid values for ``<tag>``)

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