ChromHMM
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Application data |
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| Created by | Ernst J, Kellis M |
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| Biological application domain(s) | Epigenomics |
| Principal bioinformatics method(s) | Statistical calculation |
| Created at | Massachusetts Institute of Technology |
| Maintained? | Yes |
| Programming language(s) | Java |
| Interface type(s) | Command line |
| Resource type(s) | Command-line tool |
| Licence | GPLv3 |
Summary: ChromHMM is software for learning and characterizing chromatin states.
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Description
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. ChromHMM is based on a multivariate Hidden Markov Model that explicitly models the presence or absence of each chromatin mark. The resulting model can then be used to systematically annotate a genome in one or more cell types. By automatically computing state enrichments for large-scale functional and annotation datasets ChromHMM facilitates the biological characterization of each state. ChromHMM also produces files with genome-wide maps of chromatin state annotations that can be directly visualized in a genome browser.
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