Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization-Reference-Cited by-同舟云学术

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

Published:2020-04-17 Issue:W1 Volume:48 Page:W177-W184
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Wolff Joachim¹^ORCID,Rabbani Leily²,Gilsbach Ralf³⁴⁵^ORCID,Richard Gautier⁶^ORCID,Manke Thomas²^ORCID,Backofen Rolf¹⁷^ORCID,Grüning Björn A¹^ORCID

Affiliation:

1. Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany

2. Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg im Breisgau, Germany

3. Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany

4. German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt am Main, Germany

5. Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Germany

6. INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, F-35650 Le Rheu, France

7. Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany

Abstract

Abstract 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.

Funder

German Science Foundation

Federal Ministry of Education and Research

German Research Foundation

Publisher

Oxford University Press (OUP)

Subject

Genetics

Link

http://academic.oup.com/nar/article-pdf/48/W1/W177/33433206/gkaa220.pdf

Reference43 articles.

1. Capturing chromosome conformation;Dekker;Science,2002