ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install chromhmm
and update with:
conda update chromhmm
ChromHMM comes with about 36MB of example data which is not included in the recipe. This recipe installs a script, “download_chromhmm_data.sh”, which downloads the data in the proper location, and which can be run after ChromHMM has been installed.
A Docker container is available at https://quay.io/repository/biocontainers/chromhmm.