ChromHMM specifications

Information


Unique identifier OMICS_03490
Name ChromHMM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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ChromHMM article

ChromHMM citations

 (2)
2017
PMCID: 5716071

[…] (56)., to analyze composite combinatorial interactions of the different histone ptms—in both basal and inflamed states—we employed the automated computational system for learning chromatin states chromhmm (57). chromhmm segments the genome into regions of 200 bp, such that it was possible to evaluate the presence/absence for each histone ptm according to the reads enrichment […]

2016
PMCID: 4877666

[…] 2009), and regions of enrichment were determined using macs2 (zhang et al., 2008), correcting for genome mappability. chromatin state definition and genomic feature enrichment was performed using chromhmm (ernst and kellis, 2012). capsaspora genome was reannotated as described in the supplemental experimental procedures., capsaspora cystic stage cells were transferred to fresh medium […]

ChromHMM institution(s)
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA

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