Cell Annotation Platform
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Running Differential Expression

  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.
The molecular data page with the "Selector Tool" buttons highlighted.
  1. 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.
The molecular data page with multiple cell labels highlighted.
  1. Once the cells have been selected, click the Differential Expression button to select the settings for running differential expression.
Cells selected for DE and "Differential Expression" button highlighted.
  1. 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.
Differential expression settings window.
  1. 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.
Gene table with sort by "log fold change" highlighted.
  1. 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.
Gene table and embedding with "Plot Gene Expression" button highlighted.
  1. To export the results, click Export CSV at the bottom of the gene table.
Gene table and embedding with "Export CSV" button highlighted.