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JEFworks-Lab / STdeconvolve

Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
http://jef.works/STdeconvolve/
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Question about MERFISH benchmarking #13

Closed leihouyeung closed 2 years ago

leihouyeung commented 2 years ago

Thanks for your great work. I'm wondering in the MERFISH benchmarking, how do you align the cell types of scRNA-seq which is used as a reference to the cell types of cells in MERFISH and where do you obtain the scRNA-seq data. Could you please explain this detailedly to me? Thanks.

bmill3r commented 2 years ago

Hi @leihouyeung,

Thanks for reaching out! You can read about how we performed the MERFISH benchmarking in the methods section of the preprint. We have a tutorial explaining where to download the data and the code to generate the simulated ST datasets at https://jef.works/STdeconvolve/process_mpoa_data.html. Hope this helps!

Brendan