eXamine: Visualizing annotated networks in Cytoscape [version 1; peer review: 1 approved, 3 approved with reservations]

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 in:F1000 research 2018, Vol.7, p.519
Main Authors: Spohr, Philipp, Dinkla, Kasper, Klau, Gunnar W, El-Kebir, Mohammed
Format: Article
Language:English
Subjects:
Annotations
Automation
Gene expression
Martial arts
Social networks
Social organization
User interface
Visualization
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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 7,200 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.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.14612.1