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Scran deconvolution in Flow can be invoked in Normalization and scaling section by clicking any single cell counts data node (Figure 1).

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Figure 1. Scran deconvolution task in Normalization and scaling section in Flow.

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The GUI is simple and easy to understand. The first Scran deconvolution dialog is asking to select the cluster name from a drop-down list that includes all the attributes for this dataset. The selected cluster is an optional factor specifying which cells belong to which cluster, for deconvolution within clusters (Figure 2).  Simply click the Finish button if you want to run the task as default.

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Figure 2. Interface of Scran deconvolution task in Partek Flow. Example attributes are indicated in the drop-down list if Cluster name is checked. 

The output of Scran deconvolution is a new data node that has been normalized by the pool-based size factors of each cell. We can then use this new normalized matrix for downstream analysis and visualization (Figure 3).

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Figure 3. Example workflows to demonstrate downstream analysis and visualization of Scran deconvolution output.

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