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Human Cell Atlas Integration with the Cytoscape Ecosystem for Analysis of scRNA-seq Data

Focus Portals

Project Goal

To build, and contribute to, a set of tools to address the analysis of single-cell RNA-seq data using the popular Cytoscape network analysis ecosystem.

Results & Resources

The Morris lab developed a Cytoscape app for the network analysis and visualization of single-cell RNA-seq datasets, scNetViz. This tool can read in data from EBI Single-Cell Expression Atlas and the Human Cell Atlas Data Coordination Platform, and is available on the Cytoscape app store. Additionally, they compared methods used for labeling cell types given in a particular data set to optimally choose one or more algorithms to implement into their Cytoscape app to aid in the biological interpretation of the data. The code for this benchmarking is openly available.


Lead Investigator

John Morris
John Morris