HiCEnterprise: Identifying long range chromosomal contacts in HiC data
Author and article information
Abstract
Computational analysis of chromosomal capture data is currently gaining popularity with the rapid advance in experimental techniques providing access to growing body of data. An important problem in this area is the identification of long-range contacts be- tween distinct chromatin regions. Such loops were shown to exist at different scales, either mediating interactions between enhancers and promoters or providing much longer interactions between functionally interacting distant chromosome domains. A proper statistical analysis is crucial for accurate identification of such interactions from experi- mental data. We present HiCEnterprise, a software tool for identification of long-range chromatin contacts. It implements three different sta- tistical tests for identification of significant contacts at different scales as well as necessary functions for input, output and visualization of chromosome contact matrices.
Cite this as
2019. HiCEnterprise: Identifying long range chromosomal contacts in HiC data. PeerJ Preprints 7:e27753v1 https://doi.org/10.7287/peerj.preprints.27753v1Author comment
This is a preprint version of a manuscript describing the HiCEnterprise bioinformatics software tool published here before submission to a journal.
Sections
Supplemental Information
Source code of the HiCEnterprise tool
The sourcecode as downloaded from https://github.com/regulomics/HiCEnterprise
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Hanna Kranas conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Irina Tuszyńska conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Bartek Wilczynski conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.
Data Deposition
The following information was supplied regarding data availability:
The source code is provided in the supplementary file 1 and available on github.com.
Funding
This work was supported by the grant from the Polish National Science Center [DEC 2015/16/W/NZ2/00314]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
