ChromHMM pipeline

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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Publication for ChromHMM

ChromHMM IN pipelines

 (3)
2017
PMCID: 5716071
PMID: 28981749
DOI: 10.1093/nar/gkx821

[…] (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 […]

2017
PMCID: 5716071
PMID: 28981749
DOI: 10.1093/nar/gkx821

[…] 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 against a control. the resulting […]

2015
PMCID: 4530583
PMID: 25693568
DOI: 10.1038/nature14252

[…] were within 1kb of each other. genome-wide signal coverage tracks representing per-base fold enrichment and the likelihood ratio of chip relative to control were also computed using macs2., we used chromhmm to learn combinatorial chromatin states jointly across all four conditions36. chromhmm was trained using all seven chromatin marks in virtual concatenation mode across all conditions. reads […]

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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