Question: How can I identify cells that express Gene A but not Gene B in Loupe Cell Browser?
Answer: Let's say you want to identify cells which express CD79A but not CD79B in the Acute Myeloid Leukemia (AML) tutorial dataset that comes bundled with Loupe Cell Browser (If you are new to Loupe Cell Browser, we recommend starting with the AML tutorial here).
1) Select for all cells expressing CD79A using the "Gene Expression" tab following the instructions in the tutorial (Identifying Cell Types). In this case, we obtain 716 cells that expressed CD79A and assign them to a cluster "CD79A" within the category "CellTypes".
2) Next, we do the same for cells that expressed CD79B, and assign these to a separate cluster within the same category "CellTypes".
You will notice that Step 2 created a cluster "CD79B" with 849 cells. Cells that express both CD79A and CD79B moved from cluster "CD79A" to "CD79B". This is because at this time, Loupe Cell Browser only permits cells to belong to one cluster at a time, and they are assigned to the last cluster created. Your CD79A cluster now only contains cells expressing CD79A but not CD79B. Notice that it now only contains 247 cells.
You could choose to remove the CD79B cluster from the "CellTypes" category by clicking on the trash icon as shown below. The icon appears when you hover over the CD79B cluster.