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- Once the PCA has run, click on the resultant node and select Exploratory analysis > UMAP. Run Set the UMAP parameters as defaultfollows:
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- Top 20 PCs
- Local neighborhood size 60
- Minimal distance 0.20
- While the UMAP is running we can also queue a clustering analysis. Select Exploratory analysis > Graph-based clustering. We are going to use the Leiden algorithm to cluster our data . In the (make sure to select the radio button for it). Set the number of PCs to 10. In the advanced settings, set the resolution parameter to 1e8e-4 5 and click Apply:
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