33 Select genes based on expression

Ryabhatta

Cells can be selected based on expression a gene or a set of genes in Ryabhatta. To perform this analysis

• Select the Select cells based on expression panel.
• Type in the name of the Genes of interest or the following parameters
  • nFeature_RNA to select cells based on the number of genes per cell
  • nCount_RNA to select cells based on the number of UMI counts per cell
  • percent.mt to select cells based on the percent of mitochondrial gene expression relative to total expression
• Optional select the cluster(s) where the gene-based filteration should be applied
• Press the Select the genes
• Use the sliderbars to set the threshold for each fo the genes
• Click on Select cells based on cutoff
• Optional if interested, you can use invert selection to select cells that are not selected through the cutoff.

Select cells based on expression

If you wish to select cells that express a specific set of genes and find all the markers that are correlated with this marker, then use this tool to select the cells and give them a name; for example: cells_of_interest.

Select the rest of the cells using the Invert selection option to select the rest of the cells and provide a name: rest_of_cells

Then use the differential expression to find the genes that are significantly different between the cells of interest and the rest of the cells.