Bayespace reference scRNAseq data

[chrkuo]

Thank you for creating such a wonderful tool. Quick question - I read the BayesSapce paper and I am a bit confused - can this tool be used without a reference scRNAseq data. or do I ultimately still need a scRNAseq dataset to run BayesSapce. The vignettes aren't super clear as well.

Appreciate your time

[edward130603]

Thanks for reaching out. BayesSpace does not use scRNAseq data. In the manuscript, we only used scRNAseq/deconvolution methods for validation of the BayesSpace method.

[chrkuo]

@edward130603 thank you -- since spatial transcriptomics are not single cell resolution after enhancing the clustering and resolution to subspot level - is there downstream analysis to then deconvolute that sub-spot level of resolution?

[edward130603]

We have not specifically implemented that analysis. One approach to do it would involve the following:

First predict subspot level expression using enhanceFeatures(). I suggest just doing the top HVGs rather than all genes to save compute time. Then use a deconvolution method that works on the logcounts. I believe we used CIBERSORT in the manuscript but you can try another more recent method.