histoneHMM specifications


Unique identifier OMICS_07720
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some bivariate read counts.
Output data Probabilistic classifications of genomic regions as being either modified in both samples, unmodified in both samples or differentially modified between samples.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Fortran, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.7
Stability Stable
Maintained Yes



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  • person_outline Matthias Heinig <>

Additional information


histoneHMM article

histoneHMM institution(s)
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany; Experimental Genetics Group, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany; Quantitative Epigenetics, European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Institute of Physiology, Academy of Sciences of the Czeck Republic, Prague, Czech Republic; Groningen Bioinformatics Center, University of Groningen, Groningen, The Netherlands
histoneHMM funding source(s)
Supported by funding from the EU EURATRANS award (HEALTHF4-2010-241504), by grants from the Bundesministerium für Bildung und Forschung (BMBF): GCCR and NGFN-plus Heart Failure Network and Deutsches Epigenom Programm (DEEP)’[01KU1216C], the Deutsche Forschungsgemeinschaft (DFG, HU 1522/1-1), an EMBO long-term fellowship (ALTF 1156-2009), grants from the Netherlands Organization for Scientific Research (NWO), a Rosalind Franklin Fellowship from the University of Groningen and by grant 13-04420S from the Grant Agency of the Czech Republic.

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