recipe epicseg

EpiCSeg (Epigenome Count-based Segmentation) is a software for annotating the genome based on the state of the chromatin. It provides tools for extracting count data from BAM files, typlically corresponding to ChIP-seq experiments for histone marks (but other choices are possible) it learns a statistical model for the read counts based on a HMM, it annotates the genome, and it provides tools for displaying and analyzing the obtained models and segmentations. EpiCSeg can be used as an R package or from the command line via Rscript.






package epicseg

(downloads) docker_epicseg



depends bioconductor-bamsignals:

depends bioconductor-edger:

depends bioconductor-genomicranges:

depends bioconductor-iranges:

depends bioconductor-s4vectors:

depends kfoots:

depends libgcc-ng:


depends r-base:


depends r-rcolorbrewer:

depends r-rcpp:




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 epicseg

and update with::

   mamba update epicseg

To create a new environment, run:

mamba create --name myenvname epicseg

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 `epicseg/tags`_ for valid values for ``<tag>``)

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