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.