ChromHMM: automating chromatin-state discovery and characterization. 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. 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.
Keywords for this software
References in zbMATH (referenced in 3 articles )
Showing results 1 to 3 of 3.
- Benner, Philipp; Vingron, Martin: ModHMM: a modular supra-Bayesian genome segmentation method (2019)
- Luo, Xiangyu; Wei, Yingying: Nonparametric Bayesian learning of heterogeneous dynamic transcription factor networks (2018)
- Polishko, Anton; Hasan, Md. Abid; Pan, Weihua; Bunnik, Evelien M.; Le Roch, Karine; Lonardi, Stefano: ThIEF: finding genome-wide trajectories of epigenetics marks (2017)