A typical Visium data analysis pipeline
A basic example of a spatial data analysis is outlined below.
Performing tasks in the Analyses tab
A context-sensitive menu will appear on the right side of the pipeline. Use the drop-downs in the toolbox to open available tasks for the selected data node.
An important step in analyzing single cell RNA-Seq data is to filter out low-quality cells. A few examples of low-quality cells are doublets, cells damaged during cell isolation, or cells with too few counts to be analyzed. Click here for more information on Single cell QA/QC. We will not perform Single cell QA/QC in this tutorial.
Filter Features
- Click the Filtering drop-down in the toolbox
- Click the Filter Features task
- Choose Noise reduction
- Exclude features where value <= 0.0 in at least 99.0% of the cells
- Click Finish
A task node, Filtered counts, is produced. Initially, the node will be semi-transparent to indicate that it has been queued, but not completed. A progress bar will appear on the Filter features task node to indicate that the task is running.
Normalization
- Select the Filtered Counts result node
- Choose the Normalization task from the toolbox
- Click Use recommended
- Click Finish
Exploratory analysis
- Click the Normalized counts results node
- Select the PCA task under Exploratory analysis in the toolbox
- Unselect Split by Sample
- Click Finish
- Click the PCA results node
- Select the UMAP task
- Click Finish
- Click the PCA results node
- Select the Graph-based clustering task
- Click Finish
Statistics
Additional Assistance
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