A travel guide to Cytoscape plugins

By Rintaro Saito, Michael E. Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Samad Lotia, Alexander R. Pico, Gary D. Bader, Trey Ideker. Nature Methods, 2012

1,478 citations recorded by the source corpus.

Cytoscape is open-source software for integration, visualization and analysis of biological networks. It can be extended through Cytoscape plugins, enabling a broad community of scientists to contribute useful features. This growth has occurred organically through the independent efforts of diverse authors, yielding a powerful but heterogeneous set of tools. We present a travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5–2.8. We also describe ongoing efforts to distribute, organize and maintain the quality of the collection.

Subfields: Information Systems and Management, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/eb42d8553173bf19f76f0c46357cd1fea90cf684

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Citations in the corpus

NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data (2015, methodology): “The current implementation supports fast searching, zooming and customization, together with module detection and functional enrichment analysis—the two most common needs during network analysis 28 .”
Genome-wide analysis identifies 12 loci influencing human reproductive behavior (2016, positive): “We used the Cytoscape software platform 88 , extended by the GeneMANIA plugin (data version 8/12/2014, accessed 24 April 2016) 89 .”
NetworkAnalyst - integrative approaches for protein–protein interaction network analysis and visual exploration (2014, background): “According to (31), the top two popular Cytoscape plug-ins are BiNGO (32) and MCODE (33).”
Biological interpretation of genome-wide association studies using predicted gene functions (2015, background): “Primary biliary cirrhosis [23, 13] Ventricular conduction [24, 2] Mean corpuscular volume [25, 1] Chronic kidney disease [26, 1] Corneal structure [27, 4] Phospholipid levels (plasma) [30, 1] Triglycerides [33, 4] Mean platelet volume [37, 2] Type 1 diabetes [39, 3] LDL cholesterol [40, 4] Red blood”
iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections (2014, methodology): “The iRegulon Cytoscape plugin is available via the Cytoscape App Store [27] and can be downloaded from http://iregulon.aertslab.org/.”
A practical guide to amplicon and metagenomic analysis of microbiome data (2020, methodology): “Networks could also be visualized and analyzed using R library igraph (Csardi and Nepusz, 2006), Cytoscape (Saito et al., 2012), or Gephi (Bastian et al., 2009).”
BIOLOGICAL NETWORK EXPLORATION WITH CYTOSCAPE 3 (2014, methodology): “Various network parameters may be calculated using Cytoscape’s built-in NetworkAnalyzer (via Tools → NetworkAnalyzer) (Doncheva et al. , 2012) or through Cytoscape apps such as CentiScaPe (Scardoni et al. , 2009), which calculates an even larger number of network parameters.”
FunRich: An open access standalone functional enrichment and interaction network analysis tool (2015, methodology): “:3) and MetaCore TM , some of the most commonly used free-to-use tools include DAVID [5], Cytoscape [6] and Onto-Express [7].”
Probiotics, gut microbiota, and their influence on host health and disease (2017, methodology): “Within network-based studies, Cytoscape is the most used platform to visualize and analyze interaction networks [136].”
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible (2016, background): “Cytoscape and its hundreds of apps provide numerous ways for users to interact with, visualize and analyze STRING networks (49), including integrating additional data from public repositories or their own experiments, changing visual styles and applying algorithms for network layout, clustering…”
From big data analysis to personalized medicine for all: challenges and opportunities (2015, methodology): “Both storage and computing platform such as Bioimbus [63], Bioconductor [64], CytoScape [65], are made available by scientists to exchange algorithms and data.”
Integrative approaches for finding modular structure in biological networks (2013, background): “Such differential interactions, once identified, may be further organized into modules using numerous hierarchical-or graph-clustering methods 47,134 or various Cytoscape 57 -based network analysis tools 135,136 .”
CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data (2013, methodology): “CluePedia Cytoscape plugin is freely available at http://www.ici.upmc.fr/cluepedia/ and via the Cytoscape plugin manager.”
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations (2014, background): “The download ‘PhosphoSitePlugin’ (Figure 2) is a Cytoscape plugin (21) that contains site-specific information abstracted from PSP.”