epicseg

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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.

Home http://github.com/lamortenera/epicseg
Versions 1.0
License GPL-3
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/epicseg

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install epicseg

and update with:

conda update epicseg

docker

A Docker container is available at https://quay.io/repository/biocontainers/epicseg.