AutoGeneS

AutoGeneS is a tool to automatically extracts informative genes and reveals the cellular heterogeneity of bulk RNA samples. AutoGeneS requires no prior knowledge about marker genes and selects genes by simultaneously optimizing multiple criteria: minimizing the correlation and maximizing the distance between cell types. It can be applied to reference profiles from various sources like single-cell experiments or sorted cell populations.

It is compatible with scanpy. To report issues or view the code, please refer to our github page.