The Genomic HyperBrowser is a generic web-based system for finding and testing relations between high-throughput sequencing and/or other genomic datasets, making use of statistical hypothesis testing and other advanced methodology. The system can be tried out at a publicly available main web instance.

The Genomic HyperBrowser is an extension (and thus a fork) of the Galaxy framework. For more information on the Galaxy project, see the main Galaxy Github page

Tutorials, discussion forum and news

Several public resources is available for the Genomic HyperBrowser project:

• A GitHub repository containing the latest source code
• A set of analysis guides (basic mode), examples and screencasts of the newest version of the Genomic HyperBrowser, termed GSuite HyperBrowser, are available from the main HyperBrowser server.
• A set of tutorials with screencasts for the basic HyperBrowser functionality (as available in the initial 1.0 release). (Caveat: these are rather old and not updated with recent functinality)
• A public forum for questions, opinions and feature requests
• A public announcements web page
• We also have a mailing list reserved for news (same as in the announcements page), as well as administrative messages (e.g. downtime): Mailing list and archive

About the project

The Genomic HyperBrowser (http:// hyperbrowser.uio.no) is an open-ended web server for the analysis of genome-scale data in the form of coordinates relative to reference genome assemblies, i.e. as genomic tracks. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the HyperBrowser opens for a range of genomic investigations, related to, e.g., gene regulation, disease association or epigenetic modifications of the genome.

The current version of the HyperBrowser is the result of an interdisciplinary collaboration established in late 2007, with an ambition of developing a streamlined and generic system for exploring relations between genomic features. Several sub-projects have since then been published, most notably:

• The differential disease regulome (available from the main web instance)
• HiBrowse - statistical analyses of 3D genome structure (available from a separate installation
• ClusTrack (available from the main web instance)

The GSuite HyperBrowser

The Genomic HyperBrowser has in the recent year undergone dramatic improvements focused on epigenome-wide analyses, making powerful use of user-specified suites, or collections, of related datasets. This new expansion, called the GSuite HyperBrowser, empowers researcher to ask questions about their genomic datasets in relation to the vast amount of datasets for different cell types/tissues or different epigenomic marks that has been made available from international projects like ENCODE or Roadmap Epigenomics. GSuite HyperBrowser contains user-friendly guides to answer common domain-specific questions and includes tools for defining suites of datasets, bulk downloading and analysis.

Installation

The installation procedure can be found in the HB_INSTALL.md file.

Main publications

• Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, Liestøl K, Clancy T, Ferkingstad E, Johansen M, Nygaard V, Tøstesen E, Frigessi A, Hovig E. The Genomic HyperBrowser: inferential genomics at the sequence level. Genome Biol. 2010;11(12):R121.
• Sandve GK, Gundersen S, Johansen M, Glad IK, Gunathasan K, Holden L, Holden M, Liestøl K, Nygård S, Nygaard V, Paulsen J, Rydbeck H, Trengereid K, Clancy T, Drabløs F, Ferkingstad E, Kalas M, Lien T, Rye MB, Frigessi A, Hovig E. The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W133-41.
• Paulsen J, Sandve GK, Gundersen S, Lien TG, Trengereid K, Hovig E. HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization. Bioinformatics. 2014 Jun 1;30(11):1620-2.
• Gundersen S, Kalaš M, Abul O, Frigessi A, Hovig E, Sandve GK. Identifying elemental genomic track types and representing them uniformly. BMC Bioinformatics. 2011 Dec 30;12:494.
• Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, Liestøl K, Clancy T, Drabløs F, Ferkingstad E, Johansen M, Nygaard V, Tøstesen E, Frigessi A, Hovig E. The differential disease regulome. BMC Genomics. 2011 Jul 7;12:353.
• Rydbeck H, Sandve GK, Ferkingstad E, Simovski B, Rye M, Hovig E. ClusTrack: feature extraction and similarity measures for clustering of genome-wide data sets. PLoS ONE. 2015;10(4):e0123261.

Contact information

• hyperbrowser-bugs@usit.uio.no for bug reports
• hyperbrowser-requests@usit.uio.no for other (non-public) requests

Support

This project is being developed by the Norwegian bioinformatics community as an open-source project under the GPL license v3, supported by various national and local bodies: The University of Oslo, The Norwegian Radium Hospital (OUS-HF), Statistics for Innovation (SFI2)/Norwegian Computing Center, EMBIO, Helse Sør-Øst, The Norwegian Research Council.

For further info on Norwegian bioinformatics, see www.bioinfo.no.