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const-ae / lemur

Latent Embedding Multivariate Regression
https://www.bioconductor.org/packages/lemur/
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map cell types across the latent embedding: DE testing for gene sets? #8

Closed PedroMilanezAlmeida closed 1 year ago

PedroMilanezAlmeida commented 1 year ago

I am presenting/discussing the preprint and repo in a journal club in a few minutes and thought of something... Again, pls ignore and close if this is too crazy...

Would it be possible to run the differential expression tests on several genes at a time, rather than a single gene? I was thinking maybe one could use cell type signatures in order to map cell types across the latent embedding and facilitate interpretation.

PedroMilanezAlmeida commented 1 year ago

Ugh, closing it, had nothing to do with DE analysis...

const-ae commented 1 year ago

Sorry, I am at a conference currently and didn't see your issue in time and no worries, I am excited to hear that you found the preprint interesting to discuss in your journal club :)

Would it be possible to run the differential expression tests on several genes at a time, rather than a single gene?

In theory, yes. A use case for such an approach would be to look at the expression changes across a pathway or for all downstream targets of a transcription factor, rather than a cell type signature. However, this is not an implemented analysis and would require some custom code from the analyst.