Tinyi Chu

Sorry for the delay. The quick answer is no. We need to use a comprehensive scRNA-seq reference. Please refer to the answer in this thread https://github.com/Danko-Lab/BayesPrism/issues/95#issuecomment-2287841909

Dear user, Thank you for your interest in our method. Could you kindly dump your input into an rdata file and share it with me ([email protected]) for troubleshooting? Best, Tinyi

Hi Oriol, Apologize for the delay. Thank you for your interest in our method. To answer your question, it is generally not recommended to use the known fractions due to...

Hi Oriol, Thank you for your question. To get the size factor for each cell type, simply compute the mean of the log(total library size). To convert reads fraction%, which...

This will be integrated into the next update of BayesPrism. On Tue, Oct 22, 2024 at 11:59 PM Tin Yi Chu ***@***.***> wrote: > Hi Oriol, > > Thank you...

to add to my previous reply. The size factor for each cell type should be computed at the log scale followed by taking an exponentiate, which essentially calculates the geometric...

Dear user, Thank you for your question. When clustering using deconvolved cell type-specific gene expression, it is typically expected to observe lower variance than the un-deconvolved data, and hence fewer...

You may first manually install the dependency packages in the following list: Depends: R (>= 2.6), snowfall, NMF Imports: gplots, stats, utils, scran, BiocParallel, Matrix , and then in the...

Yes. You may simply specify each individual T cell subtype as an individual cell type. It would be a good idea to have 50 or marker genes for each cell...

Hi Emmanuel, Thank you for your questions. I hope to provide some possibilities based on my guesses. First of all, log transformation should be avoided for all deconvolution methods, this...