Gephi vs Cytoscape

Struggling to choose between Gephi and Cytoscape? Both products offer unique advantages, making it a tough decision.

Gephi is a Data Visualization solution with tags like graph-theory, data-mining, social-network-analysis, open-source.

It boasts features such as Interactive visualization and exploration of network graphs, Statistical analysis tools to examine network structure and content, Algorithms for network clustering, ranking, and layout, Filtering, manipulation and partitioning of graphs, Dynamic filtering during visualization, Generation of high-quality graphical renderings for publication and pros including Free and open source, Support for large network datasets, Plugin architecture for extensibility, Cross-platform compatibility, Intuitive and flexible user interface.

On the other hand, Cytoscape is a Science & Research product tagged with network-analysis, data-visualization, graph-theory.

Its standout features include Network visualization, Analysis and statistics, Integration with gene expression data, Customizable layouts, Plugins and app store, and it shines with pros like Open source and free, Large user community, Powerful network analysis tools, Highly customizable and extensible.

Feature	Gephi	Cytoscape
Overall Score	N/A	N/A
Primary Category	Data Visualization	Science & Research

Product Overview

Gephi

Description: Gephi is an open-source network analysis and visualization software package. It allows users to interactively visualize and explore network graphs, run statistical analysis on the structure and content of the networks, and generate high-quality graphical renderings for publications.

Cytoscape

Description: Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. It provides a lot of features for network analysis and visualization.

Key Features Comparison

Gephi Features

• Interactive visualization and exploration of network graphs
• Statistical analysis tools to examine network structure and content
• Algorithms for network clustering, ranking, and layout
• Filtering, manipulation and partitioning of graphs
• Dynamic filtering during visualization
• Generation of high-quality graphical renderings for publication

Cytoscape Features

• Network visualization
• Analysis and statistics
• Integration with gene expression data
• Customizable layouts
• Plugins and app store

Pros & Cons Analysis

Gephi

Pros

• Free and open source
• Support for large network datasets
• Plugin architecture for extensibility
• Cross-platform compatibility
• Intuitive and flexible user interface

Cons

• Steep learning curve
• Limited native statistical analysis features
• Exporting high-quality images can be challenging
• Less active development compared to alternatives

Cytoscape

Pros

• Open source and free
• Large user community
• Powerful network analysis tools
• Highly customizable and extensible

Cons

• Steep learning curve
• Can be slow with large networks
• Limited native support for some file formats

Pricing Comparison

Gephi

• Open Source

Cytoscape

• Open Source