...

The GUI is simple and easy to understand. The SVD dialog is only asking to select the number of singular values to compute For each option, the grey colored description explains more details (Figure 2).  By default 100 singular values will be computed if users don't want to compute all of them.  If the dataset working on is single cell RNA-Seq, no Micro environment file is needed. However, if the dataset is spatial, most likely you would like to provide the Micro environment file because of its spatial contents. By default 0.10 will be used as threshold to select which cells are used for the analysis in the cluster. However, the number could be adjusted manually or typed in directly.  Simply click the Finish button if you want to run the task as default.

The task report for SVD is similar to PCA. Its output will be used for downstream analysis and visualization, including Harmony (Figure 3).

...