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HiCseg specifications

Information


Unique identifier OMICS_06671
Name HiCseg
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.1
Stability Stable
Requirements
R(≥2.10)
Maintained Yes

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Documentation


Publication for HiCseg

HiCseg in publications

 (6)
PMCID: 5800693
PMID: 29408904
DOI: 10.1371/journal.pone.0191899

[…] meanwhile, a resolution parameter is considered to identify tads at various scales. this algorithm has been incorporated into the software armatus []. further, a block-wise segmentation model called hicseg [] is proposed. this method reduces the problem of maximizing the likelihood with respect to the block boundaries into a 1d segmentation problem, and then employ the standard dynamic […]

PMCID: 5861416
PMID: 29272504
DOI: 10.1093/nar/gkx1246

[…] the enrichments of beaf-32, dctcf, dtfiiic, gaf and su(hw) could greatly vary depending on the tad algorithm used in drosophila (figure ). for instance, gaf presented an odds ratio (or) of 4.3 with hicseg (), an or of 4 with arrowhead (), whereas it only showed an or of 2.5 with topdom tads (). conversely, dctcf presented an or of 3.7 with hicseg, and ors around 5 with arrowhead and topdom., […]

PMCID: 5422210
PMID: 28475897
DOI: 10.1016/j.cell.2017.04.013

[…] we used hiccups v0.9 () to call loops at the following resolutions: 5kb, 10kb and 25kb. raw loop calls were processed such that we merge flanking loops into a single loop., tads were called using hicseg (). we used 10kb matrices from hic-pro as input, giving us a 10kb resolution for the tads. at this resolution hicseg becomes computationally intensive for a full chromosome. we therefore […]

PMCID: 5345799
PMID: 28282436
DOI: 10.1371/journal.pone.0172725

[…] in . interactions were binned at 10 kb resolution. contact matrices were normalised using the gothic_1.6.0 r package []. hi-c segments were identified from the normalised contact matrices using the hicseg r package [], with the lowest 10% of the linear portion of log-likelihood segment borders removed., housekeeping genes (4,091 genes) were derived from flyatlas [] selecting genes expressed […]

PMCID: 5389712
PMID: 28334773
DOI: 10.1093/nar/gkx145

[…] tools were downloaded from the providers listed in table . tools were used based on the parameters recommended by the provider, with the exception of hicseg and armatus. hicseg performed better when using the poisson distribution instead of the recommended gaussian distribution for our data set. armatus results were very sensitive to parameters […]


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HiCseg institution(s)
AgroParisTech/INRA MIA 518, Paris and UMR de Génétique Végétale, INRA/Univ Paris-Sud/CNRS, Gif-sur-Yvette, France

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