# EXPIMAP default pathway set

`pathways.gmt` is a GMT file of **Reactome** pathway gene sets ([Reactome](https://reactome.org/)), bundled so EXPIMAP can run with a sensible default when you enable the `expimap` integration method.

To use your own gene-set file instead, set the pipeline parameter **`expimap_gmt`** to the path of a GMT (or compatible) file scArches accepts.
