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A basic example of a spatial data analysis, starting from the Single cell counts node, is outlined below and is similar to a Single cell RNA-Seq analysis pipeline with the addition of the Spatial report task (shown) or Annotate Visium image task (not shown). Note that Single cell QA/QC has not been performed in this example and would be performed from the Single cell counts note with the filtered cells applied to the Single cell counts before the Filter features task. Click here for more information on Single cell QA/QC (Figure 11 pipeline). 

Performing tasks in the Analyses tab

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