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Users can click Configure to change the default settings In Advanced options (Figure 4).
Figure 4. Advanced configure options for Seurat3 integration in Flow.
Use reference to find anchors: when this box is checked, the first group of the selected attribute is used as reference to find anchors. To use a different group as reference, change the order of subgroups of the attribute in the attribute management page on Data tab. When the box is unchecked, anchors will be identified by comparing all pairs of subgroups, this option is very computationally intensive.
Perform L2 normalization: Perform L2 normalization on the CCA cell embeddings after dimensional reduction.
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