About

HiBrowse is a statistical web toolkit for analyzing, interpreting and visualizing genome-wide chromosome conformation capture data, such as Hi-C, TCC, GCC and similar. The most common types of analyses can be selected in the left panel, under "3D ANALYSIS". Alternatively, you can start by selecting a 3D track from the HyperBrowser repository, and then select an appropriate analysis as described below. You can easily upload your own 3D data to the history pane, by using a specialized data uploading tool. A range of publicly available, pre-processed 3D-datasets have allready been installed in the repository, and are ready for analysis. For help using the system, click here.

For some examples on how to use HiBrowse, see the following Galaxy Pages:

Analysing insulators

Visualization of Hi-C data

3D co-localization of evolutionary breakpoints

3D co-localization of replication origins

Comparing two Hi-C datasets

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If you use any of the HiBrowse functionality as part of a publication, please cite: Paulsen, Jonas, et al. "HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization." Bioinformatics (2014) 30 (11) 1620-1622.

If you have a genomic track, this is the place to analyze it!

To analyze a track, simply:
  1. Click Statistical analysis of tracks: Analyze genomic tracks in the left-hand menu.
  2. Select tracks from your Galaxy history of browse our collection.
    (To load a track to your history, click Get data: Upload file)
  3. Select the analysis you are interested in:
    • any property of a single track
    • any relation between a pair of tracks
For help using the system:
  1. Click The Genomic Hyperbrowser: Help in the left-hand menu.
  2. Or, look through the following screencasts:
    (further screencasts are available from the help menu)

What is
the Genomic
HyperBrowser?
Getting started Interface overview

Introduction

The Genomic HyperBrowser is a generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets. A paper on the system was published in December 2010 by Genome Biology.

GTrack

A paper identifying 15 generic track types was published in BMC Bioinformatics in December 2011. For an overview of the 15 track types, click here. The paper introduces the GTrack format, a tabular format that are able to handle all 15 track types, this in contrast to formats like BED, WIG and GFF, each covering only a handful of the track types. The Genomic HyperBrowser now supports the GTrack format and all 15 track types. The GTrack specification is available from the "Create and edit GTrack files" tool section, in addition to tools used to create, edit and validate GTrack files.

MCFDR

MCFDR is a novel algorithm for multiple hypothesis testing using the combination of sequential Monte Carlo (MC) and False Discovery Rate (FDR). MCFDR was introduced in a paper published in Bioinformatics in October 2011. The main idea is that MC sampling is stopped either by sequential MC or based on a threshold on FDR. The algorthm provides large gains in computational efficiency, and is now used for hypothesis testing in the Genomic HyperBrowser.

Differential disease regulome

A prime example of the HyperBrowser is the Differential disease regulome, mapping Transcription Factors against all human diseases. A paper on the method was published by BMC Genomics in July 2011. The Differential disease regulome can be viewed in its main version here.

Different versions of the disease regulome are available for browsing, as well as several other similar regulatory maps.

It is also easy to interactively generate a regulome on a predefined sample dataset (which of course can easily be changed to other suited data sources).

Galaxy tools

All standard tools included with the Galaxy installation are available with the HyperBrowser, under the tool header "Galaxy tools".

We currently only support basic Galaxy tools, i.e. tools that do not require installation/configuration of underlying software or genome indexes. This is primarily in order to limit the use of our server to HyperBrowser-specific runs, and also to limit maintenance. This may change at a later date. If such functionality are needed, we kindly refer to the main Galaxy server at Penn State University, or one of the other open Galaxy servers. After basic processing has been carried out, the datasets can be imported into the HyperBrowser for further analysis.
Contact information

If you have any questions, requests or comments of any kind, please use our discussion forum, available from the Help menu, or send an email to on.oiu.tisu@stseuqer-resworbrepyh‎. We are happy to respond. We especially encourage collaborative projects for further development. If you find any bugs, please send an email to on.oiu.tisu@sgub-resworbrepyh.

If you register as a user, you will get the option to subscribe to the on.oiu.tisu@ofni-resworbrepyh mailing list. Here, we will send announcements and administrative messages for users of the system. A backlog of announcements is available from the Help menu. Citation info is also available from the Help menu.

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 source code is available for download from this page.

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