Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization

被引：125

作者：

Wolff, Joachim ^{[1
]}

Rabbani, Leily ^{[2
]}

Gilsbach, Ralf ^{[3
,4
,5
]}

Richard, Gautier ^{[6
]}

Manke, Thomas ^{[2
]}

Backofen, Rolf ^{[1
,7
,8
]}

Gruening, Bjoern A. ^{[1
]}

机构：

[1] Univ Freiburg, Dept Comp Sci, Bioinformat Grp, Georges Kohler Allee 106, D-79110 Freiburg, Germany

[2] Max Planck Inst Immunobiol & Epigenet, Stubeweg 51, D-79108 Freiburg, Germany

[3] Goethe Univ, Inst Cardiovasc Physiol, Frankfurt, Germany

[4] German Ctr Cardiovasc Res DZHK, Partner Site RheinMain, Frankfurt, Germany

[5] Univ Freiburg, Fac Med, Inst Expt & Clin Pharmacol & Toxicol, Freiburg, Germany

[6] Univ Rennes, INRAE, Agrocampus Ouest, IGEPP, F-35650 Le Rheu, France

[7] Univ Freiburg, Signalling Res Ctr BIOSS, Schanzlestr 18, D-79104 Freiburg, Germany

[8] Univ Freiburg, CIBSS, Schanzlestr 18, D-79104 Freiburg, Germany

来源：

NUCLEIC ACIDS RESEARCH | 2020年 / 48卷 / W1期

关键词：

CHROMOSOME CONFORMATION CAPTURE; ORGANIZATION; PRINCIPLES; DOMAINS; GENOME;

D O I：

10.1093/nar/gkaa220

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Galaxy HiCExplorer provides a web service at https://hicexplorer.usegalaxy.eu. It enables the integrative analysis of chromosome conformation by providing tools and computational resources to pre-process, analyse and visualize Hi-C, Capture Hi-C (cHi-C) and single-cell Hi-C (scHi-C) data. Since the last publication, Galaxy HiCExplorer has been expanded considerably with new tools to facilitate the analysis of cHi-C and to provide an in-depth analysis of Hi-C data. Moreover, it supports the analysis of scHi-C data by offering a broad range of tools. With the help of the standard graphical user interface of Galaxy, presented workflows, extensive documentation and tutorials, novices as well as Hi-C experts are supported in their Hi-C data analysis with Galaxy HiCExplorer.

引用

页码：W177 / W184

页数：8

共 43 条

[1] Cooler: scalable storage for Hi-C data and other genomically labeled arrays [J].

Abdennur, Nezar ;

Mirny, Leonid A. .

BIOINFORMATICS, 2020, 36 (01) :311-316

[2] The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update [J].

Afgan, Enis ;

Baker, Dannon ;

van den Beek, Marius ;

Blankenberg, Daniel ;

Bouvier, Dave ;

Cech, Martin ;

Chilton, John ;

Clements, Dave ;

Coraor, Nate ;

Eberhard, Carl ;

Gruening, Bjoern ;

Guerler, Aysam ;

Hillman-Jackson, Jennifer ;

Von Kuster, Greg ;

Rasche, Eric ;

Soranzo, Nicola ;

Turaga, Nitesh ;

Taylor, James ;

Nekrutenko, Anton ;

Goecks, Jeremy .

NUCLEIC ACIDS RESEARCH, 2016, 44 (W1) :W3-W10

[3] Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding [J].

Andrey, Guillaume ;

Schoeflin, Robert ;

Jerkovic, Ivana ;

Heinrich, Verena ;

Ibrahim, Daniel M. ;

Paliou, Christina ;

Hochradel, Myriam ;

Timmermann, Bernd ;

Haas, Stefan ;

Vingron, Martin ;

Mundlos, Stefan .

GENOME RESEARCH, 2017, 27 (02) :223-233

[4] Community-Driven Data Analysis Training for Biology [J].

Batut, Berenice ;

Hiltemann, Saskia ;

Bagnacani, Andrea ;

Baker, Dannon ;

Bhardwaj, Vivek ;

Blank, Clemens ;

Bretaudeau, Anthony ;

Brillet-Gueguen, Loraine ;

Cech, Martin ;

Chilton, John ;

Clements, Dave ;

Doppelt-Azeroual, Olivia ;

Erxleben, Anika ;

Freeberg, Mallory Ann ;

Gladman, Simon ;

Hoogstrate, Youri ;

Hotz, Hans-Rudolf ;

Houwaart, Torsten ;

Jagtap, Pratik ;

Lariviere, Delphine ;

Le Corguille, Gildas ;

Manke, Thomas ;

Mareuil, Fabien ;

Ramirez, Fidel ;

Ryan, Devon ;

Sigloch, Florian Christoph ;

Soranzo, Nicola ;

Wolff, Joachim ;

Videm, Pavankumar ;

Wolfien, Markus ;

Wubuli, Aisanjiang ;

Yusuf, Dilmurat ;

Taylor, James ;

Backofen, Rolf ;

Nekrutenko, Anton ;

Gruening, Bjoern .

CELL SYSTEMS, 2018, 6 (06) :752-+

[5] Organization and function of the 3D genome [J].

Bonev, Boyan ;

Cavalli, Giacomo .

NATURE REVIEWS GENETICS, 2016, 17 (11) :661-678

[6] On the resemblance and containment of documents [J].

Broder, AZ .

COMPRESSION AND COMPLEXITY OF SEQUENCES 1997 - PROCEEDINGS, 1998, :21-29

[7] Functional interpretation of single cell similarity maps [J].

De Tomaso, David ;

Jones, Matthew G. ;

Subramaniam, Meena ;

Ashuach, Tal ;

Ye, Chun J. ;

Yosef, Nir .

NATURE COMMUNICATIONS, 2019, 10 (1)

[8]

Deegalla S, 2007, LECT NOTES COMPUT SC, V4881, P800

[9] Capturing chromosome conformation [J].

Dekker, J ;

Rippe, K ;

Dekker, M ;

Kleckner, N .

SCIENCE, 2002, 295 (5558) :1306-1311

[10] HiCeekR: A Novel Shiny App for Hi-C Data Analysis [J].

Di Filippo, Lucio ;

Righelli, Dario ;

Gagliardi, Miriam ;

Matarazzo, Maria Rosaria ;

Angelini, Claudia .

FRONTIERS IN GENETICS, 2019, 10

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