TopExpressingGenes

Top expressing genes for clusters of all or selected T cells.

This process finds the top expressing genes of clusters of T cells, and also performs the enrichment analysis against the genes.

The enrichment analysis is done by enrichr.

Note

There are other environment variables also available. However, they should not be used in this process. Other environment variables are used for more complicated cases for investigating top genes (See biopipen.ns.scrna.TopExpressingGenes for more details).

If you are using pipen-board to run the pipeline (see here and here), you may see the other environment variables of this process are hidden and readonly.

Environment Variables

  • dbs (list): Default: ['KEGG_2021_Human', 'MSigDB_Hallmark_2020'].
    The dbs to do enrichment analysis for significant markers See below for all libraries.
    https://maayanlab.cloud/Enrichr/#libraries
  • n (type=int): Default: 250.
    The number of top expressing genes to find.
  • subset: An expression to subset the cells for each case.