HiGlass: web-based visual exploration and analysis of genome interaction maps

Genome Biology
Peter KerpedjievNils Gehlenborg

Abstract

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 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.

References

Jun 5, 2002·Genome Research·W James KentDavid Haussler
Mar 18, 2010·Nature Methods·Cydney B NielsenTing Wang
Mar 18, 2010·Nature Methods·Nils GehlenborgAnne-Claude Gavin
Jul 20, 2010·Bioinformatics·W J KentD Karolchik
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
Sep 4, 2012·Nature Methods·Maxim ImakaevLeonid A Mirny
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
May 10, 2013·Nature Reviews. Genetics·Job DekkerLeonid A Mirny
Dec 18, 2013·Proceedings of the National Academy of Sciences of the United States of America·Jessica ZuinKerstin S Wendt
May 29, 2014·Algorithms for Molecular Biology : AMB·Darya FilippovaCarl Kingsford
Aug 28, 2014·Bioinformatics·Celine Lévy-LeducS Robin
Dec 3, 2014·Methods : a Companion to Methods in Enzymology·Bryan R LajoieNoam Kaplan
Sep 1, 2015·Bioinformatics·Caleb Weinreb, Benjamin J Raphael
Sep 4, 2015·Genome Biology·Ferhat Ay, William S Noble
Sep 12, 2015·IEEE Transactions on Visualization and Computer Graphics·Zhicheng Liu, Jeffrey Heer
Sep 24, 2015·Genome Biology·Kadir Caner Akdemir, Lynda Chin
Oct 27, 2015·Proceedings of the National Academy of Sciences of the United States of America·Adrian L SanbornErez Lieberman Aiden
Dec 2, 2015·Genome Biology·Nicolas ServantEmmanuel Barillot
Mar 5, 2016·Science·Denes HniszRichard A Young
May 24, 2016·Cell Reports·Geoffrey FudenbergLeonid A Mirny
Jul 29, 2016·Cell Systems·Neva C DurandErez Lieberman Aiden
Dec 13, 2016·Computer Graphics Forum : Journal of the European Association for Computer Graphics·S GratzlM Streit
Feb 6, 2017·Genome Biology·Galip Gürkan Yardımcı, William Stafford Noble
Mar 5, 2017·Molecular Cancer Research : MCR·Laura SeamanIndika Rajapakse
Apr 21, 2017·Nature·Georg A BusslingerJan-Michael Peters
Jun 6, 2017·Bioinformatics·Joshua S MartinYun Li
Jun 13, 2017·Nature Methods·Mattia ForcatoSilvio Bicciato
Sep 4, 2017·IEEE Transactions on Visualization and Computer Graphics·Fritz LekschasHanspeter Pfister
Sep 15, 2017·Nature·Job DekkerUNKNOWN 4D Nucleome Network
Oct 7, 2017·Cell·Suhas S P RaoErez Lieberman Aiden
Oct 21, 2017·Cell·Boyan BonevGiacomo Cavalli
Nov 3, 2017·Nature·Wibke SchwarzerFrancois Spitz
Nov 9, 2017·Nature·Chris Berdik
Jan 20, 2018·Science·Johan H GibcusJob Dekker
Feb 13, 2018·Cell Systems·James T RobinsonErez Lieberman Aiden
May 8, 2018·Cold Spring Harbor Symposia on Quantitative Biology·Geoffrey FudenbergLeonid A Mirny

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Citations

Sep 27, 2018·Annual Review of Genetics·Rafael Galupa, Edith Heard
Dec 21, 2018·Biophysics Reviews·Koustav PalFrancesco Ferrari
Jun 6, 2019·Nucleic Acids Research·Daofeng LiTing Wang
Jul 11, 2019·Bioinformatics·Nezar Abdennur, Leonid A Mirny
Dec 6, 2019·Briefings in Bioinformatics·Bohdan B KhomtchoukThemistocles L Assimes
Oct 5, 2019·Nature Communications·Jumana AlHaj AbedC-Ting Wu
Oct 18, 2019·Nature Protocols·Weixin WuSheng Zhong
May 24, 2020·International Journal of Molecular Sciences·Alexey KorablevNariman Battulin
Apr 7, 2020·ELife·Edward J BaniganLeonid A Mirny
Nov 27, 2019·Computer Graphics Forum : Journal of the European Association for Computer Graphics·S NusratN Gehlenborg
Oct 1, 2018·Arthritis Research & Therapy·Yao FuPatrick M Gaffney
Oct 24, 2019·Nature Communications·Stephanie A SchalbetterMatthew J Neale
Nov 2, 2019·Nature Communications·Joyce C K ManVincent M Christoffels
Jun 5, 2020·Nature·Flora PaldiAdele L Marston
Jun 3, 2020·Nature Communications·A Marieke OudelaarJim R Hughes
Sep 2, 2020·Nature Genetics·Di ZhangGerd A Blobel
Oct 24, 2019·Nucleic Acids Research·Fang LuYi Wang
Apr 8, 2020·Wellcome Open Research·Dan MeadMark Blaxter
Dec 19, 2019·Nature Reviews. Genetics·Rieke Kempfer, Ana Pombo
Jul 4, 2020·Bioinformatics·Jayaram KancherlaHector Corrada Bravo
Nov 11, 2020·ELife·Lorenzo CostantinoDouglas Koshland
Nov 23, 2020·Nucleic Acids Research·Jairo Navarro GonzalezW James Kent
Nov 28, 2020·Nucleic Acids Research·Kyukwang KimInkyung Jung
Jan 10, 2021·GigaScience·Kerstin HoweJonathan Wood
Aug 4, 2020·Bioinformatics·Lucille Lopez-DelisleThomas Manke
Jan 16, 2021·Current Opinion in Genetics & Development·Youngsook L JungPeter J Park
Nov 21, 2020·Wellcome Open Research·Dan MeadMark Blaxter
Jan 6, 2021·Nature Communications·Sergey V UlianovSergey V Razin
Feb 26, 2021·Scientific Reports·Anastasia RyzhkovaNariman Battulin
Mar 21, 2021·Epigenetics & Chromatin·Beoung Hun Lee, Suhn K Rhie
Apr 3, 2021·Nature Genetics·Elizabeth Ing-SimmonsJuan M Vaquerizas
Apr 9, 2021·Experimental & Molecular Medicine·Samantha Y Q OngSimon C Biddie
Apr 9, 2021·Nature·Joseph NasserJesse M Engreitz
Mar 19, 2021·G3 : Genes - Genomes - Genetics·Tomas N GeneralovicChris D Jiggins

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Methods Mentioned

BETA
Hi-C
proximity
ChIP-seq
RNA-seq
standard

Software Mentioned

domainCaller
Genome Browser
Domain Caller
Armatus
HiCseg
Integrative Genome Viewer
TADbit
Open
TADTree
Juicebox

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