Comments (4)
Hi @wangjiawen2013,
Thanks for your intest in NCEM. We support 10x visium data that was deconvoluted with a method of your choice. Important step is to export cell type abundances and cell-type specific expression values.
We recently added a tutorial how to use this data here: https://github.com/theislab/ncem_tutorials/blob/main/tutorials/type_coupling_visium.ipynb
This tutorial uses cell2location as deconvolution method on a public dataset as described here: https://github.com/theislab/ncem_benchmarks/blob/main/notebooks/data_preparation/deconvolution/cell2location_human_lymphnode.ipynb
Happy to help further.
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Hi @AnnaChristina,
Thanks for the great work of NCEM
. I have a follow-up question on applying NCEM
to Visium data. When inferring the cell-type specific expression using spot deconvolution info, we are not necessarily getting gene expression at the single-cell level. For example, we have two cells that are both cell-type A, and the cell-type specific expression of type A in a spot is the summation of two cells. Is there any implicit assumption made here when interpreting the results as cell-cell
communication?
P.S.: I saw this seems to be a relevant answer: #122 (comment)
Thank you very much!
Best,
Boyi
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Hi @AnnaChristina
Where can I download the dataset used in the tutorial ?
from ncem.
Hi @wangjiawen2013, the dataset we used for showing the usecase for Visium data can be loaded and deconvolved as described here: https://cell2location.readthedocs.io/en/latest/notebooks/cell2location_tutorial.html
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