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dkzhang777 / SlideCNA_Analysis

Vignettes for SlideCNA
MIT License
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10x & Seurat: simple vignette #2

Open floriankreten opened 4 months ago

floriankreten commented 4 months ago

Dear authors,

currently I want to compare & test different methods for CNV-calling on spatial 10x slides. Could you please provide a simple vignette for 10x data and seurat without any additional deconvolution steps? Just plain rough clustering (e.g. "tumor_cells", "reference_cells", "others") and then CNV-calling. I find it really difficult to get the inputs (metadata) into the correct format, the documentation is a bit rough to follow about that (I know that this package is quite new, so no offense here :) ).

Thanks in advance!

dkzhang777 commented 3 months ago

Hi, thank you for the feedback! Unfortunately as of now, since SlideCNA was not developed for 10x Visium which has larger spots, we are not focusing on creating a vignette for that case although in the future this may be something to look at. However, we are happy to help you out if you can pinpoint a specific problem with the metadata formatting.