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jingshuw / SAVERX

R package for transfer learning of single-cell RNA-seq denoising
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pre-trained models across technologies #8

Open igordot opened 5 years ago

igordot commented 5 years ago

Does it make sense to use pre-trained models for other technologies? For example, human immune model is based on 10x data. Can it be used for non-10x datasets? Do you know how much of an effect the dropout rate and coverage (3' or 5' versus full transcript) have?

On a related note, your publication states SAVER-X can only denoise UMI counts. Do you have any recommendations for non-UMI data? Can it perhaps be adjusted in some way?

jingshuw commented 4 years ago

SAVER-X can be used across UMI-based technologies. The reason that we can not denoise non-UMI counts is that the technical noise of non-UMI counts is very complicated, making it kind of impossible to denoise with good properties. We have tried some adjustments but have not found a universally working solution