Question: A New Version Of The Genomic Hyperbrowser Has Been Released!
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Sveinung Gundersen • 10 wrote:
Dear Galaxy users,
We are happy to announce the release of version 1.6 of the Genomic
HyperBrowser,
a analysis web server built on top of Galaxy. This release is a
companion to an
article recently published in Nucleic Acids Research, to be included
with the
2013 Webserver issue:
Sandve, Geir K., et al. "The Genomic HyperBrowser: an analysis web
server
for genome-scale data." Nucleic acids research (2013)
(http://nar.oxfordjournals.org/content/early/2013/04/29/nar.gkt342.
full)
To quote the abstract of the article:
"The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-
ended web
server for the analysis of genomic track data. 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."
In this article, an overview of most of the 42 tools and 83 analyses
included with the
Genomic HyperBrowser is presented (for the first time) in table form.
The Genomic HyperBrowser will also be presented in the 2013 Galaxy
Community
Conference (http://wiki.galaxyproject.org/Events/GCC2013), in the
Training day
workshop titled "Statistical Genome Analysis with Galaxy", and also in
a regular
talk.
The focus of this release has been on new and revamped tools:
1. A set of new tools has been added:
- Visualize track elements relative to anchor regions
- Create high-resolution map of track distribution along genome
- Create high-resolution map of multiple track distributions along
genome
- Extract segments where value is greater/less than threshold
2. A new hypothesis test for 3D-colocalization of genomic elements
has been
added (along with a tool for easier access to the analysis). This
hypothesis
tests checks whether the elements of a genomic track is positioned
on the
DNA (in interphase) closer in 3D than expected by chance. The
methodology
has been published in a separate article:
Paulsen, Jonas, et al. "Handling realistic assumptions in
hypothesis testing
of 3D co-localization of genomic elements." Nucleic acids research
(2013).
(http://nar.oxfordjournals.org/content/early/2013/04/08/nar.gkt227.
full)
Included with this analysis are readily preprocessed Hi-C datasets
for the
cell lines GM06990, GM12878, hESC, K562, and RWPE1 for human
(hg19), in
addition to cell lines cortex and mEsc for mouse (mm9), all
available in
several resolutions.
3. The usability of tools has been improved:
- The structure of the HyperBrowser tools has been rearranged, and
renamed
for easier understanding and use
- Help text and usage examples (using Galaxy Pages with embedded
histories)
has been added to most tools
4. Numerous bug fixes and improvements have been made, including the
fixing of several memory leaks.
We hope you will find the Genomic HyperBrowser and new additions
useful. Please
let us know if you experience any problems, need help with your
analysis, or
have ideas for new functionality!
For the HyperBrowser team,
Sveinung Gundersen
--
Sveinung Gundersen, PhD Student, Bioinformatics, Dept. of Tumor
Biology, Inst.
for Cancer Research, The Norwegian Radium Hospital, Montebello, 0310
Oslo,
Norway