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.
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.
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.
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.
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.
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.
Cytoscape is a well-known bioinformatics tool for displaying and exploring biological networks. The Cytoscape Ecosytem 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 braod range of applications in network anlaysis and visualization, leveraging the Cytoscape Ecosystem.
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.
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.
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.
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.
Presents a functional enrichment workflow, including: Finding networks and pathways, integrating and exploring data, performing and displaying functional enrichment analysis.
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.
Introduction to techniques for filtering and editing a network, such as applying filters to remove low-confidence edges, and performing basic network edits.
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.
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.
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.
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.
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 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.
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.
Automation
These presentations cover how to access and control Cytoscape programmatically through the CyREST interface, for example via the RCy3 package for R. Also check out Cytoscape's collection of automation scripts and notebooks.
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.
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.
Tour of Cytoscape
