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Cluster and Visualize by Gene Expression data

CITE-Seq data includes both gene and protein expression information. When the data types are combined, we can perform downstream analysis using both data types. We will begin with the mRNA data.

• Click the Merged counts data node
• Click Exploratory analysis in the toolbox
• Click Graph-based clustering 
• Click Gene Expression for Include features where "Feature type" is
• Click Configure to access the advanced settings
• Set Number of principal components to 15
• Click Apply 
  
• Click Finish to run

Once Graph-based clustering has finished running, we can visualize the results using UMAP or t-SNE. 

• Click Graph-based clustering 
• Click Exploratory analysis in the toolbox
• Click UMAP
• Click Gene Expression for Include features where "Feature type" is
• Click Configure to access the advanced settings
• Set Number of principal components to 15
• Click Apply 
  
• Click Finish to run