Running Differential Expression

The method used to calculate differential expression is similar to sc.tl.rank_genes_groups and uses the Wilcoxon test. Differential expression can be run using all the other cells as a reference or you can select a custom set of cells to use as a reference.

1. To run differential expression analysis, first select cells by using the pointer and clicking on a group of cells on the embedding or switch to using the polygon selector select the cells.

2. To select more than one cell label, click on the cell label name in the sidebar to select the first cell label and then click on additional cell labels while holding the control (PC) or command ⌘ (Mac) key on your keyboard. To cancel the selections, press the Esc key.

3. Once the cells have been selected, click the Differential Expression button to select the settings for running differential expression.

4. Select Background to run using all other cells or Custom Reference to select cells to use as a reference.
   
   For speed, the default is to perform differential expression with downsampling using a subset of cells. To perform differential expression with all cells, select All Cells. If performing differential expression with Downsampling, select a random seed for reproducibility or use the default setting of 42.

5. Once differential expression is ready, the clustered heatmap and gene table will display the results. The gene table results can sorted by log fold change or Z-score and either ascending or descending.

6. To plot the expression values or change the visibility on the heatmap of a gene, click the buttons to the left of the gene of interest.

7. To export the results, click Export CSV at the bottom of the gene table.