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Teichlab / celltypist

A tool for semi-automatic cell type classification
https://www.celltypist.org/
MIT License
260 stars 40 forks source link

Genes driving the prediction #45

Closed cdiaz45 closed 1 year ago

cdiaz45 commented 1 year ago

Hello, as usual thank you so much for all your help with my questions. I am wondering if there is a way to know which genes are driving a specific similarity with a model? Can I get that information from the results? Many thanks, Carmen

ChuanXu1 commented 1 year ago

@cdiaz45, as indicated in the tutorial, the driving genes of each cell type is solely based on training dataset / model. You can obtain the markers using the extract_top_markers function. Is this what you are asking?

cdiaz45 commented 1 year ago

Ah no problem. I actually built the model using all of the genes so I wanted to see which ones contributed the most. A friend suggested to look at the beta coefficient (although I am repeating his words), so I wanted to see if it was possible to extract those. I saw you have several versions on how to build the model so will try different ones and check how much that changes the predictions. Thank you though. Amazing work and tool.