Home
 Tour of Cytoscape
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| 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. |
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Basic Data Visualization
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RNA-Seq Data Analysis
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Differentially Expressed Genes
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| Evaluating expression data in the context of networks. | Workflow for network analysis of differentially expressed genes from an RNA-Seq experiment. | Network analysis workflow for differentially expressed genes. |
| Cytoscape Apps | Data Visualization | Importing Data | Network Analysis | Exporting and Publishing |
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| 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 |
| Introduction | Visualization | Automation | Modules |
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| Introductory presentations | Visualization of networks and data | Automation presentations | Presentation modules |
Learn how to create your own Cytoscape protocol using our Making Cytoscape Tutorials protocol.
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.
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.
| stringApp |
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| 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 |
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| Presents three workflows for visualizing experimental data on pathways from WikiPathways and using the built-in ID mapping functionality of Cytoscape to support data overlays. Workflows include a basic use case, working with multiple pathways and a network analysis scenario. |
| Enrichment Table |
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| The Enrichment Table App provides the functionality of functional enrichment analysis for any network loaded into Cytoscape using g:Profiler's web service. |
| EnrichmentMap Pipeline |
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| 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. |
| scNetViz - Single-cell RNASeq analysis |
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| This tutorial includes two basic use cases, working with data from the EMBL-EBI Single Cell Expression Atlas, or local data. After loading the data into Cytoscape from local files or through the browser, we will generate plots from the data, perform differential expression analysis, generating networks from the top genes, and functionally characterize and visualize the networks. |
| Legend Creator |
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| Describes how to use the Legend Creator App to generate legends representing the visual mappings used in network visualizations. |
| Cytoscape and NDEx |
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| In this tutorial, you will learn how to find networks in NDEx, load networks into Cytoscape and export networks to NDEx. |
| Cytoscape Ecosystem Tutorial |
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| Cytoscape is a well-known bioinformatics tool for displaying and exploring biological networks. The Cytoscape Ecosystem extends beyond the desktop software to include web apps (like cytoscape.js), community-contributed collections of networks (NDEx) and apps (AppStore), and the CyREST programmatic interface. Programmatic access and interactive display via R, Python and JS enable a broad range of applications in network analysis and visualization, leveraging the Cytoscape Ecosystem. |
| clusterMaker App |
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| The clusterMaker app provides functionality for clustering, dimensionality reduction and ranking. This tutorial describes how the various algorithms can be used together to explore a data set and how to integrate it with other Cytoscape apps and capabilities, using two types of data; protein-protein interaction data from the STRING database, and expression data from a yeast heat shock experiment. |
| Basic Data Visualization |
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| Presents a scenario of how expression data can be assessed in the context of networks to tell a biological story through data visualization. |
| Network Layout |
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| Overview of automatic layout algorithms in Cytoscape and how to apply layouts. |
| Custom Graphics and Labels |
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| Overview of using Custom Graphics to add graphs, charts and other graphics to nodes. |
| Group Nodes |
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| Overview of how to use node grouping functions to manipulate graphs. |
| Advanced Visualization: Adjusting the View |
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| A short protocol describing how to adjust the network view. |
| Advanced Visualization: Style Properties |
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| A short protocol describing advanced style options. |
| Advanced Visualization: Working with Palettes |
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| A short protocol describing how to work with color palettes. |
| Advanced Visualization: Tuning Layouts |
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| A short protocol describing how to tune layout algorithms. |
| Advanced Visualization: Node Position |
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| A short protocol describing the use of node position. |
| Advanced Visualization: Graphics |
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| A short protocol describing how to add graphics to nodes. |
| Advanced Visualization: Working with Annotations |
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| A short protocol describing how to add annotations in Cytoscape. |
| Advanced Visualization: Animations |
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| A short protocol describing how to use animations in Cytoscape. |
| Advanced Visualization: Font Properties |
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| A short protocol reviewing options for font properties. |
| Loading Networks |
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| This tutorial describes the details of importing an existing network and applying a layout. |
| Importing Data From Tables |
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| This tutorial describes how to import expression data from a spreadsheet, and how to link it to already loaded networks. |
| Importing Network From Table |
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| This tutorial describes how to import a network from tabular data. |
| Identifier Mapping |
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| This protocol will show you how to map or translate identifiers from one database to another, to facilitate data visualization. |
| Differentially Expressed Genes Network Analysis |
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| 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 |
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| 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. |
| RNA-Seq Data Network Analysis |
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| Describes a network analysis workflow for differentially expressed genes from an RNA-Seq experiment. |
| Protein Interaction Analysis Using Cytoscape and NDEx |
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| 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 |
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| Demonstrates network retrieval from the STRING database, basic analysis, TCGA data loading and visualization. |
| EnrichmentMap Pipeline |
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| 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 |
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| Presents a functional enrichment workflow, including: Finding networks and pathways, integrating and exploring data, performing and displaying functional enrichment analysis. |
| Pathway Figure Gene Set Analysis |
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| This protocol describes how to visualize data on the gene set extracted from a published pathway figure, create a network from it, perform functional enrichment, and include the original figure for comparison. |
| Filtering by Selection |
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| Introduction to techniques for filtering and editing a network, such as applying filters to remove low-confidence edges, and performing basic network edits. |
| Saving Results |
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| Overview of options for saving and exporting results from Cytoscape. |
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 and Network Biology - University of California at San Francisco, 5 March 2024 |
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| 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 Omics Analysis - ISMB/ECCB 2021, July 22-23, 2021 |
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| An introduction to Cytoscape as part of the ISMB/ECCB tutorial on Reproducible omics data analysis workflows. |
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, 7 March 2024 |
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| 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 |
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| 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 |
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| Visualizing and Analyzing Biological Networks with STRING and Cytoscape. |
| Single Cell Network Visualization - Gladstone & University of California San Francisco, March 2021 |
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| With the scNetViz app, you can access single-cell RNA-seq datasets from EBI and HCA atlases or load your own count matrixes and then generate cell plots (tSNE, UMAP), perform differential expression (DE) analysis, generate heatmaps and violin plots, and reconstruct interaction networks from your top DE genes per cluster or category. Data overlay and enrichment analysis in Cytoscape is also facilitated by the app. |
These presentations cover how to access and control Cytoscape programmatically through the CyREST interface, via RCy3 (R) and py4cytoscape (Python). Also check out Cytoscape's collection of automation scripts and notebooks.
| Advanced Automation in Cytoscape - Virtual, San Francisco, May 2023 |
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| Learn how to access and control Cytoscape from R and Python. 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 |
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| Cytoscape Automation in R using Rcy3 |
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 |
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| Introduction to Cytoscape including Cytoscape Apps, network and data loading and exporting visualizations. |
| Intro to Network Biology |
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| Introduction to Network Biology. Review of networks applications in research. |
| Finding Network Data |
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| Finding Network Data. Review of public network and pathway databases accessible from Cytoscape. |
| Network Analysis |
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| Network Analysis. Review of analytical approaches and tools. |
| Network Visualization |
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| Network Visualization. Network depiction, data mapping, layouts and animation. |
| Advanced Visualization |
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| Advanced Visualization: Tips and tricks. |
| Complexes |
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| Enriching PPI networks with complexes: Sources of protein complex data and using complex data in Cytoscape. |
| Group Visualization |
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| Working with Groups in Cytoscape. Manipulating groups, groups visualization and configuration. |
| Ten Simple Rules |
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| From Ten simple rules to create biological network figures for communication (manuscript in review) . |
| Network Taxonomy |
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| Network Taxonomy. Pathways, Interactions and Similarity. |
| Network Visualization Challenge |
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| Making sense out of biological networks. |
| PPI Data Sources |
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| PPI Data Sources. Reviews public sources of PPI data, including relevant experimental techniques, computational techniques and public repositories. |
Contact Cytoscape Help Desk with any questions about Cytoscape usage.
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