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federicomarini / quantiseqr

https://federicomarini.github.io/quantiseqr/
GNU General Public License v3.0
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Manually curated signatures #23

Closed france-hub closed 1 year ago

france-hub commented 1 year ago

Ciao!

Thanks for this package. I was wondering whether quantiseqr allows manually curated signatures for the immune deconvolution.

Thank you Francesco

federicomarini commented 1 year ago

Hi Francesco,

In theory it does - the parameter is in for that reason. @FFinotello is the main designer of the signatures and their structure, I am tagging her in here to notify her. I cannot really help you too much on this, as I stepped into the project at a later point to make it Bioc-ready 😉 Federico

FFinotello commented 1 year ago

Ciao Francesco,

Unfortunately, quanTIseq does not support user-provided signatures, due to its approaches to account for cell-type-specific mRNA abundance and CD4-Treg multicollinearity, both of which are based on the TIL10 signature matrix.

I hope this helps despite the negative outcome, Francesca

france-hub commented 1 year ago

Ok, thank you both for your answers!

Best, Francesco

federicomarini commented 1 year ago

I hope I did not mislead you into thinking otherwise. But as Francesca nicely put, quantiseqr (and quanTIseq) work like a charm with the TIL10 signature matrix. There would be some advanced steps to take care of to enable other signatures to work "out of the box", and I guess the plan was to not put this burden on the users.

france-hub commented 1 year ago

Oh, no. I got your point and understand.

Thank you!