Table of Contents |
---|
maxLevel | 2 |
---|
minLevel | 2 |
---|
exclude | Additional Assistance |
---|
|
A typical Visium data analysis pipeline
A basic example of a spatial data analysis is outlined below.
![](/download/attachments/73466222/image2023-12-11_20-33-32.png?version=2&modificationDate=1702393762131&api=v2)
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.
![](/download/attachments/73466222/image2023-12-11_18-26-12.png?version=1&modificationDate=1702337172878&api=v2)
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
![](/download/attachments/73466222/image2023-12-11_18-7-5.png?version=1&modificationDate=1702336759127&api=v2)
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.
![](/download/attachments/73466222/image2023-12-11_18-22-48.png?version=1&modificationDate=1702336969219&api=v2)
Normalization
- Select the Filtered Counts result node
- Choose the Normalization task from the toolbox
![](/download/attachments/73466222/image2023-12-11_20-1-22.png?version=1&modificationDate=1702342883201&api=v2)
- Click Use recommended
- Click Finish
![](/download/attachments/73466222/image2023-12-11_19-56-0.png?version=1&modificationDate=1702342560848&api=v2)
Exploratory analysis
- Click the Normalized counts results node
- Select the PCA task under Exploratory analysis in the toolbox
- Unselect Split by Sample
- Click Finish
![](/download/attachments/73466222/image2023-12-11_20-11-58.png?version=1&modificationDate=1702343518520&api=v2)
- Click the PCA result node
- Select the Graph-based clustering task
- Click Finish
![](/download/attachments/73466222/image2023-12-11_20-37-5.png?version=1&modificationDate=1702345026213&api=v2)
- Click the Graph-based clustering result node
- Select the UMAP task
- Click Finish
![](/download/attachments/73466222/image2023-12-11_20-14-24.png?version=1&modificationDate=1702343664733&api=v2)
Statistics