SC transform task performs the normalization method of R package sctransform [1]

We recommend perform sctransform normalization on single cell row count data node. Select SCTransfrom task in Normalization and scaling section on the pop-up menu to invoke the dialog (Figure 1)

Figure 1. When a data node containing a single cell count matrix is selected, SCTransform is available in the toolbox

By default, it will generate report on all the input features. When uncheck the Report all features, user can specify a certain number of features with highest variance in the report.

In the Advanced option, when click Configure to change the default settings (Figure 2)

Figure 2. Use the mean or median of all samples as the baseline to normalize the data

References

1. Christoph Hafemeister, Rahul Satija Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression.  https://doi.org/10.1101/576827

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