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dkzhang777 / SlideCNA

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SlideCNA for 10x visium #1

Open jefferyUstc opened 1 year ago

jefferyUstc commented 1 year ago

Hi, Nice work it is! Is this applicable for 10x visium data?

Thanks!

dkzhang777 commented 1 year ago

Hi,

Theoretically this should be applicable to 10x Visium, though we have not tested it on Visium yet. If using for Visium, I'd recommend decreasing the avg_bead_per_bin parameter from 12 to a smaller number to avoid bins that consolidate too many cells (tradeoff between signal and resolution) since Visium captures more cells per spot.