Tools for Research: Network Analysis

Gephi

Gephi website

Gephi is an open source program to explore network graphs and node and link diagrams. The program helps identify clusters, algorithmically arranges the network for readability, and helps visualize change over time. The program also lets you customize the view with colors, labels, grouping, and filtering.

• What you'll need:

  • No programming needed but Java required

• Accepted file formats:

  • There is a data processing wizard, but the underlying data must contain a node table and an edge table that you can identify. There are instructions to help. 

    • CSV

    • Excel

    • Additional supported graph formats 

• Examples/gallery:

  • Gephi Flicker

• License: Open source

• Help:

  • Gephi Quick Start Tutorial

  • Gephi Quick Start Guide

Cytoscape

Cytoscape website

Cytoscape is a Java-based open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.  Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps / plugins.

• What You'll Need:
  • Current version of Java
• Examples/Ideas:
  • Tutorials on Network Analysis with Cytoscape
  • Cytoscape Tutorials
  • Networking with Cytoscape
• Licensing: Open Source
• Help:
  • Release Notes
  • Open Tutorials
  • Help Forum

NodeXL

NodeXL Website

NodeXL Basic is a free, open-source template for Microsoft® Excel® 2007, 2010, 2013 and 2016 that makes it easy to explore network graphs.  With NodeXL, you can enter a network edge list in a worksheet, click a button and see your graph, all in the familiar environment of the Excel window.

• What You'll Need:
  • Microsoft Excel
• Examples
• License: NodeXL Pro is a fee-based fully featured version of NodeXL that includes access to social media network data importers, advanced network metrics, and automation. 
• Help 

igraph

igraph website

igraph is a collection of open-source network analysis tools with the emphasis on efficiency, portability, and ease of use. The igraph network-analysis package can be used with R, Python, C/C++.

• What you’ll need:
  • Programming skills in R, Python or C.
• Examples
• License:  Open source
• Help:
  • igraph github
  • igraph tutorial