HMMSeg statistics

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HMMSeg specifications

Information


Unique identifier OMICS_02597
Name HMMSeg
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for HMMSeg

HMMSeg in publications

 (6)
PMCID: 5643431
PMID: 29038551
DOI: 10.1038/s41598-017-13196-4

[…] analysis algorithms., the following analysis was performed using r. to identify individual cell types, the ihc images were processed by a custom hidden markov model (hmm) classification system, hmmseg. to train the system, pixels of dark brown (dab), dark purple (cd31), and deep blue (hematoxylin) color were manually collected from regions of ihc stained tissue. to obtain higher quality […]

PMCID: 5429574
PMID: 28499350
DOI: 10.1186/s12864-017-3764-9

[…] from significant limitations. for instance, some supervised learning methods cannot find de novo information. some unsupervised learning methods train on small genomic regions such as segway [] and hmmseg [], or output a single mark’s probability such as chomhmm []. none of these algorithms explicitly compare targets of a specific tf with different histone modification marks to qualitatively […]

PMCID: 4557131
PMID: 26282110
DOI: 10.1038/ncomms8973

[…] as our understanding of epigenomics has progressed, previous methods have leveraged histone combinations to partition the epigenome into various chromatin states, such as chromhmm, segway and hmmseg. the resulting analyses enabled by chromatin state analysis has provided fruitful findings about epigenomic variation and lineage specification. however, no methods have yet been developed […]

PMCID: 3400636
PMID: 22829947
DOI: 10.1371/journal.pone.0041374

[…] function of ctcf-binding sites as domain barriers, we identified the heterochromatin and euchromatin domains across the genome using diverse histone modifications and open chromatin as inputs to hmmseg, a hidden markov model-based segmentation for parameter learning and region calling ( and ). this analysis revealed, in k562 cells, a total of 14,166 euchromatin domains typically ranged […]

PMCID: 3213131
PMID: 22102821
DOI: 10.1371/journal.pgen.1002334

[…] ratios for each sample were transformed into z-scores. these z-scores were then classified as “increased”, “normal”, or “decreased” in copy number using a three-state hmm. the hmm was applied using hmmseg . for each sample, hmm state assignments of probes were merged into segments if consecutive probes of the same state less than 50 kbp apart. if two segments of the same state were separated […]


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HMMSeg institution(s)
Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA

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