Generate group cell counts

If a single cell data node contains cell attribute information, e.g., clustering results, classifications, or imported attributes, a counts-type data node containing the number of cells from each attribute group for each sample can be generated and used for downstream analysis.

To invoke Generate group cell counts:

• Click a single cell count data node with cell-level attribute information

• Click Pre-analysis tools in the toolbox

• Click Generate group cell counts

• Select the attribute to group the cells from the Group by drop-down menu (Figure 1)

• Click Finish

Figure 1. Select an attribute to group cells

A group cell counts node will be generated. The data node contains a matrix of cell counts in each sample for each group. You can view the counts results in the Group cell counts report (Figure 2).

Figure 2. Group cell counts for each sample are listed in the task report

The Cell counts data node is a counts type data node and downstream analysis tasks, such as normalization, PCA, and ANOVA, can be used to analyze the group cell counts data.

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