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Kristina Hanspers edited this page Feb 7, 2018 · 35 revisions
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This is a collection of protocols for Cytoscape and Cytoscape Apps, ranging from introductory training to advanced analysis.

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Many apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases.

Categories

Data Visualization Importing Data Network Analysis Exporting and Publishing
Data Visualization Importing Data Network Analysis Exporting and Publishing
Transforming tables into network visualizations to tell a biological story Loading networks and datasets from a variety of sources Using topology and graph theory to make sense of networks Saving and sharing your work effectively

Sharing

Please feel free to use, share, copy or adapt any of the training materials you find here. They are all implicitly published under the CC0 waiver for maximum reuse potential.

PDFs

You can produce PDFs of any protocol by simply appending ?print-pdf to the end of the base url (example) and then print or save as PDF in landscape orientation for the best result.

Protocols

Data Visualization

Basic Data Visualization
Presents a scenario of how expression and network data can be combined to tell a biological story and includes these concepts: Visualizing networks using expression data, filtering networks based on expression data and assessing expression data in the context of a biological network.
Pathway Data Visualization
Presents a basic workflow for visualizing experimental data on pathways, using the WikiPathways App and the built-in IdMapper functionality.
Mapping Data
Outlines the common use of expression data in Cytoscape to set the visual attributes of the nodes in a network. The result is a powerful visualization, portraying functional relation and experimental response at the same time.

Importing Networks and Tables

Loading Network Data
This tutorial describes the details of importing an existing network and applying a layout.
Loading Omics Data
This tutorial describes how to load expression data from a spreadsheet, and how to link it to already loaded networks.

Network Analysis

Functional Enrichment
Presents a functional enrichment workflow. Key aspects covered in this tutorial include: Retrieving networks and pathways, integrating and exploring your data, performing functional enrichment analysis, and functional interpretation and display.
Filtering and Editing
Introduction to techniques for filtering and editing a network, such as applying filters to remove low-confidence edges, and performing basic network edits.
Selecting subnetworks
Introduction to the technique of selecting subnetworks to assist with functional interpretation of the network.

Exporting and Publishing

Saving Results
Overview of options for saving and exporting results from Cytoscape.

Questions

Contact Cytoscape Help Desk with any questions about Cytoscape usage.

To report any issues with the tutorial content, click "Issues" above and open a new issue.