Ruth Isserlin edited this page Aug 2, 2018 · 59 revisions

Cytoscape is an open source bioinformatics platform for visualizing molecular interaction networks and integrating these with expression profiles and other high throughput data sets. This is a collection of protocols, tutorials and workflows for Cytoscape and Cytoscape Apps, ranging from introductory training to advanced analysis.

Our protocols are organized into categories below. Complete listings are available here: presentations, modules and protocols. For automation examples, check out the collection of scripted workflows.

For Cytoscape automation documentation and sample scripts, see Cytoscape automation home

Getting Started

Tour of Cytoscape
New to Cytoscape? Our "Tour of Cytoscape" tutorial gives you a high-level introduction to Cytoscape's capabilities and features, and directs you to detailed training content for each step.

Recommended Exercises

Basic Data Visualization Functional Enrichment
Presents a scenario of how expression data can be assessed in the context of networks to tell a biological story through data visualization. Presents a functional enrichment workflow, including: Finding networks and pathways, integrating and exploring data, performing and displaying functional enrichment analysis.

Categories

Cytoscape Apps Data Visualization Importing Data Network Analysis Exporting and Publishing
Cytoscape Apps Data Visualization Importing Data Network Analysis Exporting and Publishing
How to use apps in your research Transforming tables into network biology visualizations 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

Cytoscape Apps

stringApp
Provides exercises for importing networks from the STRING database via simple queries from within Cytoscape, as well as layout, data overlays, enrichment analysis and more.
WikiPathways App
Presents a basic workflow for visualizing experimental data on pathways from WikiPathways and using the built-in ID mapping functionality of Cytoscape to support data overlays.

Data Visualization

Basic Data Visualization
Presents a scenario of how expression data can be assessed in the context of networks to tell a biological story through data visualization.
Visualizing 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.
Network Layout
Overview of automatic layout algorithms in Cytoscape and how to apply layouts.

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, including: Finding networks and pathways, integrating and exploring data, performing and displaying functional enrichment analysis.
Filtering by Selection
Introduction to techniques for filtering and editing a network, such as applying filters to remove low-confidence edges, and performing basic network edits.
EnrichmentMap Pipeline
A step-by-step protocol explaining how to complete pathway enrichment analysis using g:Profiler (filtered gene list) and GSEA (unfiltered, whole genome, ranked gene list), followed by visualization and interpretation using EnrichmentMap in Cytoscape.

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.

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