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ICE specifications

Information


Unique identifier OMICS_00521
Name ICE
Alternative name Iterative Correction and Eigenvector decomposition
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Leonid A Mirny

Publication for Iterative Correction and Eigenvector decomposition

ICE citations

 (11)
library_books

Orientation dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome

2018
Nat Commun
PMCID: 5899087
PMID: 29654302
DOI: 10.1038/s41467-018-03694-y

[…] rences in sequencing depth and data sparsity due to allelic-specific read assignment. This transformation was performed as described in ref. , except that the transformation was performed on the ICE (iterative correction and eigenvector decomposition)-normalized contact matrices rather than the observed-over-expected matrices because we did not wish to normalize out the distance effect. […]

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

[…] s of each read. We filtered out redundant and non-uniquely mapped reads, 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

Advances in Genomic Profiling and Analysis of 3D Chromatin Structure and Interaction

2017
Genes
PMCID: 5615356
PMID: 28885554
DOI: 10.3390/genes8090223

[…] n its central region, and normally such a structural entity ranges from kilo- to mega-basepairs. Since the current 3C-based sequencing data is inevitably contaminated with systematic biases, the ICE (iterative correction and eigenvector decomposition) technique was proposed to identify the local chromatin states, global chromosomal interactions, and the conserved chromatin organization []. To infe […]

call_split

Kmt1e regulates a large neuron specific topological chromatin domain

2017
Nat Genet
PMCID: 5560095
PMID: 28671686
DOI: 10.1038/ng.3906
call_split See protocol

[…] nd, self-cycle, and single-end pairs are not retained. Binning was performed in 40kb and 100kb non-overlapping, adjacent windows across the genome and resulting contact matrices were normalized using iterative correction and eigenvector decomposition (ICE) as previously described.Starting with the 20 kb resolution intra-chromosomal contact matrices generated by HiC-Pro, we first generated 100 kb r […]

library_books

Long range control of gene expression via RNA directed DNA methylation

2017
PLoS Genet
PMCID: 5438180
PMID: 28475589
DOI: 10.1371/journal.pgen.1006749

[…] ined replicates as an alternate, deeper view of the data (, ).In order to obtain high confidence / stringent interactions, we also used a published interaction caller—Fit-Hi-C with ICE normalization (iterative correction and eigenvector decomposition) () [,] which is stringent but not sensitive enough to work with the limited sequencing coverage available for individual biological repeats. We exam […]

library_books

Multi scale chromatin state annotation using a hierarchical hidden Markov model

2017
Nat Commun
PMCID: 5385569
PMID: 28387224
DOI: 10.1038/ncomms15011

[…] ucture, we analyse a public high-resolution Hi-C data set. The chromatin interaction hubs are identified as described previously, Briefly, we first normalize the raw interaction matrix using the ICE (Iterative Correction and Eigenvector Decomposition) algorithm. Then, we identify statistically significant chromatin interactions by using Fit-Hi-C. We rank the 5 kb segments by the interaction freque […]

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ICE institution(s)
Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA

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