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Integrated genome browser: visual analytics platform for genomics

Identifieur interne : 000732 ( Ncbi/Curation ); précédent : 000731; suivant : 000733

Integrated genome browser: visual analytics platform for genomics

Auteurs : Nowlan H. Freese ; David C. Norris ; Ann E. Loraine

Source :

Bioinformatics [ 1367-4803 ] ; 2016.

RBID : PMC:4937187

Abstract

Motivation: Genome browsers that support fast navigation through vast datasets and provide interactive visual analytics functions can help scientists achieve deeper insight into biological systems. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser.

Results: Here we describe multiple updates to IGB, including all-new capabilities to display and interact with data from high-throughput sequencing experiments. To demonstrate, we describe example visualizations and analyses of datasets from RNA-Seq, ChIP-Seq and bisulfite sequencing experiments. Understanding results from genome-scale experiments requires viewing the data in the context of reference genome annotations and other related datasets. To facilitate this, we enhanced IGB’s ability to consume data from diverse sources, including Galaxy, Distributed Annotation and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data.

Availability and implementation: IGB is open source and is freely available from http://bioviz.org/igb.

Contact:aloraine@uncc.edu

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937187

DOI: 10.1093/bioinformatics/btw069
PubMed: 27153568
PubMed Central: 4937187

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Le document en format XML

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<author><name sortKey="Freese, Nowlan H" sort="Freese, Nowlan H" uniqKey="Freese N" first="Nowlan H." last="Freese">Nowlan H. Freese</name>
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<front><div type="abstract" xml:lang="en"><p><bold>Motivation:</bold>
 Genome browsers that support fast navigation through vast datasets and provide interactive visual analytics functions can help scientists achieve deeper insight into biological systems. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser.</p>
<p><bold>Results:</bold>
 Here we describe multiple updates to IGB, including all-new capabilities to display and interact with data from high-throughput sequencing experiments. To demonstrate, we describe example visualizations and analyses of datasets from RNA-Seq, ChIP-Seq and bisulfite sequencing experiments. Understanding results from genome-scale experiments requires viewing the data in the context of reference genome annotations and other related datasets. To facilitate this, we enhanced IGB’s ability to consume data from diverse sources, including Galaxy, Distributed Annotation and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data.</p>
<p><bold>Availability and implementation:</bold>
 IGB is open source and is freely available from <ext-link ext-link-type="uri" xlink:href="http://bioviz.org/igb">http://bioviz.org/igb</ext-link>
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<p><bold>Contact:</bold>
<email>aloraine@uncc.edu</email>
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Integrated genome browser: visual analytics platform for genomics

Integrated genome browser: visual analytics platform for genomics

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Abstract

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