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Alexander Pico edited this page Feb 27, 2020 · 102 revisions

Getting Started

Tour of Cytoscape
New to Cytoscape? This 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 Differentially Expressed Genes
Presents a scenario of how expression data can be assessed in the context of networks to tell a biological story through data visualization. Describes a network analysis workflow in Cytoscape for a set of differentially expressed genes. Includes retrieving relevant networks, network functional enrichment analysis and integration and visualization of experimental data.

Protocols

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

Presentations

Introduction Visualization Automation Modules
Introduction Visualization Automation Modules
Introductory presentations Visualization of networks and data Automation presentations Presentation modules

Join the Community

Create your own Cytoscape protocol

Learn how to create your own Cytoscape protocol using our Making Cytoscape Tutorials protocol.

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.
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.
Legend Creator
Describes how to use the Legend Creator App to generate legends representing the visual mappings used in network visualizations.

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.
Custom Graphics and Labels
Overview of using Custom Graphics to add graphs, charts and other graphics to nodes.

Importing Networks and Tables

Loading Networks
This tutorial describes the details of importing an existing network and applying a layout.
Importing Data From Tables
This tutorial describes how to import expression data from a spreadsheet, and how to link it to already loaded networks.
Importing Network From Table
This tutorial describes how to import a network from tabular data.
Identifier Mapping
This protocol will show you how to map or translate identifiers from one database to another, to facilitate data visualization.

Network Analysis

Differentially Expressed Genes Network Analysis
Describes a network analysis workflow in Cytoscape for a set of differentially expressed genes. Includes retrieving relevant networks, network functional enrichment analysis and integration and visualization of experimental data.
Affinity Purification-Mass Spectrometry Network Analysis
This protocol describes how to use data from an affinity purification-mass spectrometry experiment to to generate relevant interaction networks, enriching the networks with information from public resources, analyzing the networks and creating effective visualizations.
Protein Interaction Analysis Using Cytoscape and NDEx
This protocol describes how to use Cytoscape, NDEx, and NDEx Integrated Query (IQuery) to work with protein interaction data. It covers some of the same topics as the AP-MS protocol above, starting with the same dataset but describes the use of NDEx, coupled with IQuery, as a source of reference networks, relevant pathways, and drug, disease, and tissue-association information, plus the use of NDEx as means for storing and sharing analysis results.
Variant Data Analysis
Demonstrates network retrieval from the STRING database, basic analysis, TCGA data loading and visualization.
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.
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.

Exporting and Publishing

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

Presentations

Introduction

Basic introductions to network biology and Cytoscape for a variety of research applications. This is a great place to start if you are new to the joy of networks.

Introduction to Cytoscape for Biologists - University of California at San Francisco, 12 February 2020
An introduction to Network Biology and how to use Cytoscape. Review of the major applications of network biology; How to finding relevant networks and pathways; Importing your data; Network analyses, layout and visualization; Example workflows.
Introduction to Cytoscape for Computer Scientists - University of California at San Francisco, 21 February 2020
An introduction to Network Biology and how to develop applications in the Cytoscape Ecosytem. Review of the major applications of network biology; Introduction to Cytoscape and network analysis and visualization; Focus on describing the desktop, scripting and cloud-based ecosystem, including how to develop your own applications within the ecosystem.
Data Analysis & Visualization in Cytoscape - University of California at San Francisco, October 2019
Computational analysis of protein-protein interactions: Sequences, networks and diseases.

Visualization

These talks focus on the challenge of data visualization and the benefits of using networks to meet these challenges. Cytoscape provides a tons of features dedicated to network visualization.

Data visualization with Cytoscape - University of California at San Francisco, February 2020
Dive deeper into data visualization with Cytoscape. Learn some approaches to effective communication through network visualizations; Master network layouts and data visualization; Learn some of the new, advanced visualization features of Cytoscape; Know where to find relevant Cytoscape apps and tutorials.
Network Visualization - Flatiron Institute, New York, October 2017
Network Visualization with Cytoscape. Identify relevant types and sources of networks; various approaches to network visualization; when and how to use Cytoscape; publish, share and export networks online.
Cytoscape and STRING - University of Copenhagen, Copenhagen, November 2018
Visualizing and Analyzing Biological Networks with STRING and Cytoscape.

Automation

These presentations cover how to access and control Cytoscape programmatically through the CyREST interface, for example via the RCy3 package for R.

Advanced Automation in Cytoscape - Marshall University, West Virginia, March 2019
Learn how to access and control Cytoscape from R or any programming language. Integrate Cytoscape into your bioinformatics pipelines involving any type of data and network analysis or visualization challenge.
Cytoscape Automation in R using RCy3 - BioC, 2018, Toronto
Cytoscape Automation in R using Rcy3

Modules

These modular sets of slides cover isolated topics and are meant to be resused and combined into proper presentations (like the ones listed above). Browse these before you make your own and please consider contributing your presentation modules here for others to reuse.

Intro to Cytoscape
Introduction to Cytoscape including Cytoscape Apps, network and data loading and exporting visualizations.
Intro to Network Biology
Introduction to Network Biology. Review of networks applications in research.
Finding Network Data
Finding Network Data. Review of public network and pathway databases accessible from Cytoscape.
Network Analysis
Network Analysis. Review of analytical approaches and tools.
Network Visualization
Network Visualization. Network depiction, data mapping, layouts and animation.
Advanced Visualization
Advanced Visualization: Tips and tricks.
Complexes
Enriching PPI networks with complexes: Sources of protein complex data and using complex data in Cytoscape.
Group Visualization
Working with Groups in Cytoscape. Manipulating groups, groups visualization and configuration.
Ten Simple Rules
From Ten simple rules to create biological network figures for communication (manuscript in review) .
Network Taxonomy
Network Taxonomy. Pathways, Interactions and Similarity.
Network Visualization Challenge
Making sense out of biological networks.
PPI Data Sources
PPI Data Sources. Reviews public sources of PPI data, including relevant experimental techniques, computational techniques and public repositories.

Questions

Contact Cytoscape Help Desk with any questions about Cytoscape usage.

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