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HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps

View ORCID ProfilePeter Kerpedjiev, View ORCID ProfileNezar Abdennur, View ORCID ProfileFritz Lekschas, View ORCID ProfileChuck McCallum, Kasper Dinkla, Hendrik Strobelt, View ORCID ProfileJacob M Luber, Scott Ouellette, Alaleh Azhir, Nikhil Kumar, Jeewon Hwang, Soohyun Lee, View ORCID ProfileBurak H Alver, View ORCID ProfileHanspeter Pfister, View ORCID ProfileLeonid A Mirny, View ORCID ProfilePeter J Park, View ORCID ProfileNils Gehlenborg
doi: https://doi.org/10.1101/121889
Peter Kerpedjiev
1Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Nezar Abdennur
2Computational and Systems Biology Program, MIT, Cambridge, USA
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Fritz Lekschas
3School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
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Chuck McCallum
1Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Kasper Dinkla
3School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
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Hendrik Strobelt
3School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
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Jacob M Luber
1Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
4Bioinformatics and Integrative Genomics Program, Harvard Medical School, Boston, MA, USA
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Scott Ouellette
1Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Alaleh Azhir
1Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Nikhil Kumar
1Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Jeewon Hwang
3School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
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Soohyun Lee
1Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Burak H Alver
1Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Hanspeter Pfister
3School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
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Leonid A Mirny
5Department of Physics, MIT, Cambridge, USA
6Institute for Medical Engineering and Science, MIT, Cambridge, USA
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Peter J Park
1Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Nils Gehlenborg
1Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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  • For correspondence: nils@hms.harvard.edu
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Abstract

In the face of new multidimensional genomic data, visual tools are essential for exploring data, discovering patterns, and rationalizing and disseminating results. Within the field of genomics, this pursuit is often confounded by not only the size of the data but the variety of scales at which features are visible. Genome-wide interaction maps produced by Chromosome Conformation Capture techniques such as Hi-C are particularly challenging as patterns emerge at a range of scales from kilobases to hundreds of megabases. Since automatic detection and classification of these features yield ambiguous results, visual exploration and assessment is essential for analysis of Hi-C data and its comparison with other genomic tracks, requiring navigation and comparison across multiple loci, multiple resolutions and multiple samples. Here we present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, allowing users to combine various data types, synchronize multiple visualization modalities, and effortlessly share fully customizable views with others. We demonstrate its utility in exploring different experimental conditions, comparing the results of analyses, and creating interactive snapshots to share with collaborators and the broader public. HiGlass is accessible online at http://higlass.io and is also available as a containerized application that can be run on any platform.

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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. It is made available under a CC-BY 4.0 International license.
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Posted October 30, 2017.
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HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps
Peter Kerpedjiev, Nezar Abdennur, Fritz Lekschas, Chuck McCallum, Kasper Dinkla, Hendrik Strobelt, Jacob M Luber, Scott Ouellette, Alaleh Azhir, Nikhil Kumar, Jeewon Hwang, Soohyun Lee, Burak H Alver, Hanspeter Pfister, Leonid A Mirny, Peter J Park, Nils Gehlenborg
bioRxiv 121889; doi: https://doi.org/10.1101/121889
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HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps
Peter Kerpedjiev, Nezar Abdennur, Fritz Lekschas, Chuck McCallum, Kasper Dinkla, Hendrik Strobelt, Jacob M Luber, Scott Ouellette, Alaleh Azhir, Nikhil Kumar, Jeewon Hwang, Soohyun Lee, Burak H Alver, Hanspeter Pfister, Leonid A Mirny, Peter J Park, Nils Gehlenborg
bioRxiv 121889; doi: https://doi.org/10.1101/121889

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