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The Genomic HyperBrowser: an analysis web server for genome-scale data
2013
Nucleic Acids Research
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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
2010
Genome Biology
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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]
2016
bioRxiv
pre-print
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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
2017
GigaScience
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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
2021
F1000Research
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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
2014
Computer applications in the biosciences : CABIOS
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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
2011
BMC Genomics
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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
2014
Cell Regeneration
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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]
2016
Msphere
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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
2012
Genome Biology
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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
2015
PLoS ONE
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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
2015
Cold Spring Harbor Protocols
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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
2020
Frontiers in Genetics
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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
2015
BMC Research Notes
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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
2011
BMC Bioinformatics
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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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