xy-chen16/stplus

stPlus: reference-based enhancement of spatial transcriptomics

stplus's Issues

Academic query for code

Hello~shengquan, I recently read your paper "stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics". I think stPlus is very useful for reference. However, I got many errors when I run Seurat and liger, I have tried many ways to solve it, but it has not been solved yet. Could you please upload your R code? thanks

No option for cpu

My system have very old NVIDIA card, that pytorch don't support. I want to run on cpu but there is no option in stPlus.

Question about data processing.

Hi, I'm interesting about your work. But I'm not a expert on bio, there have some question I want to ask, I'll appreciate it if you can help me.

Let begin with data, does your cell in spatial data means spot?

Suppose spatial_df have n gene with m spots, scRNA have k gene with l cells. First you pad 0 on spatial_df on gene to get spatial_df have k gene with m spots.

Then what confused me is how merge and shuffle done. Do the two of them sort alternately? like this[scRNA[0], spatial_df[0], scRNA[1], spatial_df[1], ..., scRNA[m], spatial_df[m], scRNA[m+1], scRNA[l]].

Do I understand correctly? The question is why do like this?

I hope you can help me! Thanks a lot.