Recently, I use chromHMM to analyze the chromatin states but it can only generate the chromatin states and signal files respectively. It can not generate the read counts density and chromatin states together. So I wanna ask guys that do we have a pipeline or R package for processing the chromatin states via ChIP-seq data or damid, etc.? Then I can acquire a matrix or something and I could generate the development of chromatin states from loose to tight.