eXamine: Visualizing annotated networks in Cytoscape

eXamine is a Cytoscape app that displays set membership as contours on top of a node-link layout of a small graph. In addition to facilitating interpretation of enriched gene sets of small biological networks, eXamine can be used in other domains such as the visualization of communities in small soc...

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Bibliographic Details
Published inF1000 research Vol. 7; p. 519
Main Authors Spohr, Philipp, Dinkla, Kasper, Klau, Gunnar W, El-Kebir, Mohammed
Format Journal Article
LanguageEnglish
Published England F1000 Research Limited 2018
F1000 Research Ltd
Subjects
Software Tool
enrichment
graph drawing
visualization
network community
Euler diagram
functional subnetwork modules
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Summary:eXamine is a Cytoscape app that displays set membership as contours on top of a node-link layout of a small graph. In addition to facilitating interpretation of enriched gene sets of small biological networks, eXamine can be used in other domains such as the visualization of communities in small social networks. eXamine was made available on the Cytoscape App Store in March 2014, has since registered more than 7,700 downloads, and has been highly rated by more than 25 users. In this paper, we present eXamine's new automation features that enable researchers to compose reproducible analysis workflows to generate visualizations of small, set-annotated graphs.
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No competing interests were disclosed.
KD and PS implemented the automation features of eXamine. MEK and GWK supervised the project. GWK, KD, MEK and PS wrote the paper. All authors read and approved the manuscript.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.14612.2