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The Genomic HyperBrowser: an analysis web server for genome-scale data

Geir K. Sandve, Sveinung Gundersen, Morten Johansen, Ingrid K. Glad, Krishanthi Gunathasan, Lars Holden, Marit Holden, Knut Liestøl, Ståle Nygård, Vegard Nygaard, Jonas Paulsen, Halfdan Rydbeck (+9 others)
2013 Nucleic Acids Research  
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.  ...  The Genomic HyperBrowser web server provides a broad suite of functionality for rigorous statistical analysis of genomic data.  ... 
doi:10.1093/nar/gkt342 pmid:23632163 pmcid:PMC3692097 fatcat:tvgsi43iofe5zartiypzpyzmmu

The Genomic HyperBrowser: inferential genomics at the sequence level

Geir K Sandve, Sveinung Gundersen, Halfdan Rydbeck, Ingrid Glad, Lars Holden, Marit Holden, Knut Liestol, Trevor Clancy, Egil Ferkingstad, Morten Johansen, Vegard Nygaard, Eivind Tostesen (+2 others)
2010 Genome Biology  
The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power.  ...  The Genomic HyperBrowser implements the approach and is available at http://hyperbrowser.uio.no.  ...  Acknowledgements We gratefully acknowledge ChIP-chip data provision from Florian M Pauler, and helpful comments on the manuscript from Magnus Lie Hetland, Sylvia Richardson and Håvard Rue.  ... 
doi:10.1186/gb-2010-11-12-r121 pmid:21182759 pmcid:PMC3046481 fatcat:hlwkdn2t5vakdirac3fvybtmf4

GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome [article]

Boris Simovski, Daniel Vodak, Sveinung Gundersen, Diana Domanska, Abdulrahman Azab, Lars Holden, Marit Holden, Ivar Grytten, Knut Dagestad Rand, Finn Drablos, Morten Johansen, Antonio Mora (+12 others)
2016 bioRxiv   pre-print
The GSuite HyperBrowser is an open-source system for streamlined acquisition and customizable statistical analysis of large collections of genome-wide datasets.  ...  We present GSuite HyperBrowser, the first comprehensive solution for integrative analysis of dataset collections across the genome and epigenome.  ...  GSuite HyperBrowser is an open-source, web-based system that enables analysis of a broad array of both hypothesis-driven and data-driven questions that may be posed using large collections of genomic tracks  ... 
doi:10.1101/067561 fatcat:hy4loclp6nexvm46pmwn373hgi

GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome

Boris Simovski, Daniel Vodák, Sveinung Gundersen, Diana Domanska, Abdulrahman Azab, Lars Holden, Marit Holden, Ivar Grytten, Knut Rand, Finn Drabløs, Morten Johansen, Antonio Mora (+13 others)
2017 GigaScience  
We present GSuite HyperBrowser, the first comprehensive solution for integrative analysis of dataset collections across the genome and epigenome.  ...  The GSuite HyperBrowser is an open-source system for streamlined acquisition and customizable statistical analysis of large collections of genomewide datasets.  ...  GSuite HyperBrowser is an open-source, web-based system that enables analysis of a broad array of both hypothesis-driven and data-driven questions that may be posed using large collections of genomic tracks  ... 
doi:10.1093/gigascience/gix032 pmid:28459977 pmcid:PMC5493745 fatcat:xbliaifhk5blzgo7y7ndlvrj4q

Recommendations for the FAIRification of genomic track metadata

Sveinung Gundersen, Sanjay Boddu, Salvador Capella-Gutierrez, Finn Drabløs, José M. Fernández, Radmila Kompova, Kieron Taylor, Dmytro Titov, Daniel Zerbino, Eivind Hovig
2021 F1000Research  
We demonstrate practical usage by importing datasets through TrackFind into existing examples of relevant analytical tools for genomic tracks: EPICO and the GSuite HyperBrowser.  ...  Many types of data from genomic analyses can be represented as genomic tracks, i.e. features linked to the genomic coordinates of a reference genome.  ...  Acknowledgements We thank Abdulrahman Azab and Geir Kjetil Sandve for contribution to the track data import tool in GSuite HyperBrowser, which inspired this work. lxxvi http://www.imi.europa.eu/  ... 
doi:10.12688/f1000research.28449.1 pmid:34249331 pmcid:PMC8226415 fatcat:n5xal7ssrjf4jaybqfyoygcmia

HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization

Jonas Paulsen, Geir Kjetil Sandve, Sveinung Gundersen, Tonje G. Lien, Kai Trengereid, Eivind Hovig
2014 Computer applications in the biosciences : CABIOS  
Understanding the organization of chromatin in three dimensions is a crucial next step in the unraveling of global gene regulation, and methods for analyzing such data are needed.  ...  Software is implemented in Python, and source code is available for download by following instructions on the main site.  ...  server for genome-scale data.  ... 
doi:10.1093/bioinformatics/btu082 pmid:24511080 pmcid:PMC4029040 fatcat:3dz2b2othjgypnhn6jxfrwhcty

The differential disease regulome

Geir K Sandve, Sveinung Gundersen, Halfdan Rydbeck, Ingrid K Glad, Lars Holden, Marit Holden, Knut Liestøl, Trevor Clancy, Finn Drabløs, Egil Ferkingstad, Morten Johansen, Vegard Nygaard (+3 others)
2011 BMC Genomics  
Furthermore, existing pipelines for related large-scale analysis are tailored for particular sources of input data, and there is a need for generic methodology for integrating complementary sources of  ...  We further believe our approach to genome analysis could allow an advance from the current typical situation of one-time integrative efforts to reproducible and upgradable integrative analysis.  ...  We also thank PubGene Inc. for kind assistance in the development of literature tracks. Additional funding was  ... 
doi:10.1186/1471-2164-12-353 pmid:21736759 pmcid:PMC3160420 fatcat:7dqotix26zgotcwa6zudc7huza

glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data

Andrew Paul Hutchins, Ralf Jauch, Mateusz Dyla, Diego Miranda-Saavedra
2014 Cell Regeneration  
on genomic interval data and support for the efficient random access to huge genomic data files.  ...  Genomic datasets and the tools to analyze them have proliferated at an astonishing rate.  ...  Acknowledgements We thank Chu Lee Thean for valuable usage reports and testing of early versions of glbase.  ... 
doi:10.1186/2045-9769-3-1 pmid:25408880 pmcid:PMC4230833 fatcat:34fwqm5crncj5cpd3dep3qvbii

Bioinformatics Analysis of Estrogen-Responsive Genes [chapter]

Adam E. Handel
2016 Msphere  
Combining transcriptomic and ChIP-seq data enables a distinction to be drawn between direct and indirect estrogen target genes.  ...  The expression of many genes is regulated through the steroid hormone receptors ESR1 and ESR2. These bind to DNA and modulate the expression of target genes.  ...  Figure 3 illustrates this Fig. 1 Uploading files to the Galaxy/Genomic HyperBrowser server.  ... 
doi:10.1007/978-1-4939-3127-9_4 pmid:26585125 pmcid:PMC5065092 fatcat:6cq2reomovfixnjh4yl7qprbxq

EpiExplorer: live exploration and global analysis of large epigenomic datasets

Konstantin Halachev, Hannah Bast, Felipe Albrecht, Thomas Lengauer, Christoph Bock
2012 Genome Biology  
Here we describe EpiExplorer, a web tool for exploring genome and epigenome data on a genomic scale.  ...  We demonstrate EpiExplorer's utility by describing a hypothesis-generating analysis of DNA hydroxymethylation in relation to public reference maps of the human epigenome.  ...  Epigenomics consortia for helpful discussions, the members of the Bast group for supporting the  ... 
doi:10.1186/gb-2012-13-10-r96 pmid:23034089 pmcid:PMC3491424 fatcat:dweegccdeveafmccvgbwtq7qaq

ClusTrack: Feature Extraction and Similarity Measures for Clustering of Genome-Wide Data Sets

Halfdan Rydbeck, Geir Kjetil Sandve, Egil Ferkingstad, Boris Simovski, Morten Rye, Eivind Hovig, Ali Torkamani
2015 PLoS ONE  
Clustering is a popular technique for explorative analysis of data, as it can reveal subgroupings and similarities between data in an unsupervised manner.  ...  HyperBrowser server: http://hyperbrowser.uio.no/hb/.  ...  Provided the gene ontology data: HR. Developed the software: GKS BS. Provided the histone methylation data: MR.  ... 
doi:10.1371/journal.pone.0123261 pmid:25879845 pmcid:PMC4400084 fatcat:xhdu7zmtozaa7gynxm3zgsbgyi

Online Resources for Genomic Analysis Using High-Throughput Sequencing

Daniel Blankenberg, James Taylor, Anton Nekrutenko
2015 Cold Spring Harbor Protocols  
Here we describe the use and applications of common file formats for coding and storing genomic data, consider several web-accessible open-source resources for the visualization and analysis of NGS data  ...  As a consequence, several online resources and communities have been developed to assist researchers with both the management and the analysis of sequencing data sets.  ...  The Department specifically disclaims responsibility for any analyses, interpretations, or conclusions.  ... 
doi:10.1101/pdb.top083667 pmid:25655493 fatcat:ooet5nofajciro52qzauyo25ka

epiCOLOC: Integrating Large-Scale and Context-Dependent Epigenomics Features for Comprehensive Colocalization Analysis

Yao Zhou, Yongzheng Sun, Dandan Huang, Mulin Jun Li
2020 Frontiers in Genetics  
with queries for genomic regions.  ...  Colocalization analysis determines whether genomic features are functionally related to a given search and will facilitate identifying the underlying biological functions characterizing intricate relationships  ...  SUPPLEMENTARY MATERIAL The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fgene.2020. 00053/full#supplementary-material  ... 
doi:10.3389/fgene.2020.00053 pmid:32117461 pmcid:PMC7029718 fatcat:gwud7dwdvre45ejiqqwzmrl77i

Automated amplicon design suitable for analysis of DNA variants by melting techniques

Per Olaf Ekstrøm, Sigve Nakken, Morten Johansen, Eivind Hovig
2015 BMC Research Notes  
Results: We have constructed a web-based tool that is able to batch design DNA variant assay suitable for analysis by denaturing gel/capillary electrophoresis and high resolution melting.  ...  Although DNA sequencing has had an exponential decrease in cost per base pair analyzed, focused and target-specific methods are however still much in use for analysis of DNA variants.  ...  Competing interests The authors declare that they have no competing interests.  ... 
doi:10.1186/s13104-015-1624-8 pmid:26559640 pmcid:PMC4642734 fatcat:ta4ppgdbz5bnba6ip4syusrnim

Identifying elemental genomic track types and representing them uniformly

Sveinung Gundersen, Matúš Kalaš, Osman Abul, Arnoldo Frigessi, Eivind Hovig, Geir Sandve
2011 BMC Bioinformatics  
We thus propose two unified formats for track data, an improved XML format, BioXSD 1.1, and a new tabular format, GTrack 1.0.  ...  The variation in biological context, and the increasingly dispersed mode of data generation, imply a need for precise, interoperable and flexible representations of genomic features through formats that  ...  We thank Kai Trengereid for crucial work in developing the GTrack-related tools, and Inge Jonassen for valuable input on the BioXSD format.  ... 
doi:10.1186/1471-2105-12-494 pmid:22208806 pmcid:PMC3315820 fatcat:uq63xf6tzrf25jha7t2osog56m
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