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Software tools for visualizing Hi-C data

Galip Gürkan Yardımcı, William Stafford Noble
doi: https://doi.org/10.1101/086017
Galip Gürkan Yardımcı
aDepartment of Genome Sciences University of Washington
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William Stafford Noble
bDepartment of Genome Sciences Department of Computer Science and Engineering University of Washington
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Abstract

Recently developed, high-throughput assays for measuring the three-dimensional configuration of DNA in the nucleus have provided unprecedented insights into the relationship between DNA 3D configuration and function. However, accurate interpretation of data from assays such as ChIA-PET and Hi-C is challenging because the data is large and cannot be easily rendered using a standard genome browser. In particular, an effective Hi-C visualization tool must provide a variety of visualization modes and be capable of viewing the data in conjunction with existing, complementary data. We review a number of such software tools that have been described recently in the literature, focusing on tools that do not require programming expertise on the part of the user. In particular, we describe HiBrowse, Juicebox, my5C, the 3D Genome Browser, and the Epigenome Browser, outlining their complementary functionalities and highlighting which types of visualization tasks each tool is best designed to handle.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted November 07, 2016.
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Software tools for visualizing Hi-C data
Galip Gürkan Yardımcı, William Stafford Noble
bioRxiv 086017; doi: https://doi.org/10.1101/086017
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Software tools for visualizing Hi-C data
Galip Gürkan Yardımcı, William Stafford Noble
bioRxiv 086017; doi: https://doi.org/10.1101/086017

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