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HiCNorm specifications

Information


Unique identifier OMICS_03491
Name HiCNorm
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Jun Liu

Publication for HiCNorm

HiCNorm citations

 (10)
library_books

3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations

2017
Nat Commun
PMCID: 5715138
PMID: 29203764
DOI: 10.1038/s41467-017-01793-w

[…] fig. ). these results indicate that raw interaction counts in cancer hi-c data are biased by cnvs and should be corrected to obtain per-copy chromosome interaction map. we compared the ice and hicnorm methods for normalizing the interaction matrix. ice can better correct the cnv bias than hicnorm (fig.  and supplementary fig. ), so we used it to obtain normalized hi-c matrices […]

library_books

Condensin mediated remodeling of the mitotic chromatin landscape in fission yeast

2017
Nat Genet
PMCID: 5621628
PMID: 28825727
DOI: 10.1038/ng.3938

[…] source of these non-proximity factors. instead, it operates on the principle that all genomic regions should be equally visible and partake in an equal number of interactions. the second technique, hicnorm, attempts to remove the impact of three non-proximity factors known to affect observed interactions, fragend frequency, gc content and mappability. the iteratively-corrected normalized […]

library_books

An integrated model for detecting significant chromatin interactions from high resolution Hi C data

2017
Nat Commun
PMCID: 5442359
PMID: 28513628
DOI: 10.1038/ncomms15454

[…] read count bias, including a non-parametric probabilistic approach due to yaffe and tanay and iterative correction and eigenvalue decomposition (ice), which approximates this method. more recently, hicnorm was introduced to learn these biases statistically with poisson regression, using gc content and other features as covariates in a generalized linear model (glm) for interaction bin counts. […]

library_books

Capturing genomic relationships that matter

2017
PMCID: 5346121
PMID: 28078515
DOI: 10.1007/s10577-016-9546-4

[…] analytical pipelines have been developed that employ two main normalisation tactics. one approach models the effects of each bias separately and has been taken by the hicpipe (yaffe and tanay ) and hicnorm (hu et al. ) pipelines, applied to hi-c libraries. whilst it has not been used in the analysis of capture hi-c libraries, these models could be extended with the inclusion of an extra […]

library_books

Interactome transcriptome analysis discovers signatures complementary to GWAS Loci of Type 2 Diabetes

2016
Sci Rep
PMCID: 5067504
PMID: 27752041
DOI: 10.1038/srep35228

[…] regions may control distant genes through long-range interactions. we used chromosome conformation capture (hi-c) data to test this hypothesis. using two independent normalization methods, hicnorm and yaffe to identify consensus interacting partners in k562 and gm06990 cell lines, we identified the chromatin region containing rs1635852 and other diagram-snps reaching genome-wide […]

library_books

Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions

2016
Nucleic Acids Res
PMCID: 4797302
PMID: 26869583
DOI: 10.1093/nar/gkw070

[…] https://noble.gs.washington.edu/proj/yeast-architecture/sup.html. we performed explicit-factor normalization of this contact data to control for gc content, mappability and fragment length using hicnorm () genome-wide (chromosome by chromosome) as per () and then generated a new 3d reconstruction using the constrained optimization approach (). the hicnorm source code was downloaded […]


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HiCNorm institution(s)
Department of Statistics, Harvard University, Cambridge, MA, USA

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