More than 3000 genes

[sarah-chapin]

In the CellOracle Tutorial, we are advised not to use more than 3000 genes, as it might cause problems in the downstream analysis. Are the anticipated problems related to memory usage, or will using more genes actually cause errors in the simulation?

Thanks.

[KenjiKamimoto-ac]

Using more genes will not cause errors if you have abundant computational resources. We recommend filtering out non-variable genes because it is challenging to do meaningful modeling with lowly expressed and low-variable genes.