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Modify a set of genes for a set of cells from real scRNA-seq data to create a synthetic dataset #68

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siyao-liu opened this issue Dec 6, 2024 · 3 comments

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@siyao-liu
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Hello!

I was wondering if it would be possible to use scDesign3 to modify a set of genes for a set of cells from a real scRNAseq dataset to create a synthetic dataset? If so, how? Thanks very much!

@SONGDONGYUAN1994
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Dear Siyao,

I did not fully get your question. I think you can select some genes and cells and only fit the model on this submatrix, and then alter the model. Please check our step-by-step mode in our vignittee.

Best regards,
Dongyuan

@siyao-liu
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@SONGDONGYUAN1994 Thanks for your quick response. Sorry if I didn't describe my question clear enough for you. What I really want to do is to create a new cell type in the simulated data by modifying a set of genes from the existing real dataset. Do you think scDesign3 can do that? Thank you! Following your tutorial here https://songdongyuan1994.github.io/scDesign3/docs/articles/scDesign3-cellType-vignette.html, it seems that scDesgin3 can only take a real dataset and create a synthetic with the same cell types or varying their cell type proportions. Could scDesign create a new cell type from real data? Thank you!

@SONGDONGYUAN1994
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Hi Siyao,

It depends on your definition of a new cell type. In https://songdongyuan1994.github.io/scDesign3/docs/articles/scDesign3-introduction-vignette.html , we describe the step-by-step mode. Eventually, you will input your own parameter matrix in function simu_new. Of course you can create new cell types and add them into the simu_new.

Best,
Dongyuan

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