eXamine: Visualizing annotated networks in Cytoscape [version 1; referees: 1 approved, 2 approved with reservations]

Mohammed El-Kebir, Philipp Spohr, Kasper Dinkla, Gunnar W. Klau

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Article number519
JournalF1000Research
Volume7
DOIs
StatePublished - Jan 1 2018

Keywords

  • Enrichment
  • Euler diagram
  • Functional subnetwork modules
  • Graph drawing
  • Network community
  • Visualization

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

Fingerprint Dive into the research topics of 'eXamine: Visualizing annotated networks in Cytoscape [version 1; referees: 1 approved, 2 approved with reservations]'. Together they form a unique fingerprint.

  • Cite this