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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

 (9)
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

[…] ads, and kept the reads within 500 bp upstream of enzyme cutting sites (HindIII or Mbol) due to the size selection. We utilized the iterative correction and eigenvector decomposition (ICE) method and HiCNorm to normalize raw interaction matrices and compared their effect on correcting CNV bias. […]

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

[…] e 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 matrice […]

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 variable […]

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

[…] d gene-gene relationships to assess the utility of these interactome signatures as anti-diabetic drug targets. The Chromatin interaction (Hi-C) data of K562 and GM06990 cell lines were analyzed using HiCNorm and Yaffe’s method, and consensus interacting chromatin regions identified by both normalization methods in both cell lines were used. […]

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

[…] from 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 from http: […]

call_split

Impact of data resolution on three dimensional structure inference methods

2016
BMC Bioinformatics
PMCID: 4744395
PMID: 26852142
DOI: 10.1186/s12859-016-0894-z
call_split See protocol

[…] n fitting tREX, tPAM, and BACH to the simulation data, we normalized the data by incorporating the systematic bias information as covariates to the model. In contrast, we first normalized the data by HiCNorm [] before using ShRec3D, ChromSDE and PASTIS to the normalized data. In order to assess and compare estimation accuracy of the methods, we need to take into account the fact that the estimated […]

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

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