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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Detalles Bibliográficos
Autores principales: Spohr, Philipp, Dinkla, Kasper, Klau, Gunnar W., El-Kebir, Mohammed
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2018
Materias:
Software Tool Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013758/
https://www.ncbi.nlm.nih.gov/pubmed/29983924
http://dx.doi.org/10.12688/f1000research.14612.2
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author Spohr, Philipp
Dinkla, Kasper
Klau, Gunnar W.
El-Kebir, Mohammed
author_facet Spohr, Philipp
Dinkla, Kasper
Klau, Gunnar W.
El-Kebir, Mohammed
author_sort Spohr, Philipp
collection PubMed
description 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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spelling pubmed-60137582018-07-06 eXamine: Visualizing annotated networks in Cytoscape Spohr, Philipp Dinkla, Kasper Klau, Gunnar W. El-Kebir, Mohammed F1000Res Software Tool Article 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. F1000 Research Limited 2018-07-05 /pmc/articles/PMC6013758/ /pubmed/29983924 http://dx.doi.org/10.12688/f1000research.14612.2 Text en Copyright: © 2018 Spohr P et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Tool Article
Spohr, Philipp
Dinkla, Kasper
Klau, Gunnar W.
El-Kebir, Mohammed
eXamine: Visualizing annotated networks in Cytoscape
title eXamine: Visualizing annotated networks in Cytoscape
title_full eXamine: Visualizing annotated networks in Cytoscape
title_fullStr eXamine: Visualizing annotated networks in Cytoscape
title_full_unstemmed eXamine: Visualizing annotated networks in Cytoscape
title_short eXamine: Visualizing annotated networks in Cytoscape
title_sort examine: visualizing annotated networks in cytoscape
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013758/
https://www.ncbi.nlm.nih.gov/pubmed/29983924
http://dx.doi.org/10.12688/f1000research.14612.2
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