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HiCseg specifications


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
Maintained Yes


No version available


Publication for HiCseg

HiCseg citations


Sequence based multiscale modeling for high throughput chromosome conformation capture (Hi C) data analysis

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 […]


TAD free analysis of architectural proteins and insulators

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., […]


The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension

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 […]


Regions of very low H3K27me3 partition the Drosophila genome into topological domains

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 […]


A critical assessment of topologically associating domain prediction tools

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 […]


Analysis methods for studying the 3D architecture of the genome

PMCID: 4556012
PMID: 26328929
DOI: 10.1186/s13059-015-0745-7

[…] are consistent across different resolutions. both the resolution-specific domains and the consensus domains are then used as tad calls for downstream analysis. another dynamic programming method, hicseg, computes the optimal segmentation into tads via a maximum likelihood formulation []. however, hicseg does not readily allow identification of multiscale or hierarchical domains., to make use […]

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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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