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Yelab2020 / Cottrazm

Construct Tumor Transition Zone Microenvironment
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Tumour Boundary with Leiden partitioning #18

Open ConDem94 opened 1 month ago

ConDem94 commented 1 month ago

Hi, thank you for this amazing package!

I have tried running STInferCNV with random_trees but it is taking way too long even with CPUs = 30 in my University's cluster. Is there another way to reduce running speed with this method?

I then ran leiden method and was much faster. Do you have a modified script to identify the TumorBoundaries using the leiden method? Although this method does not generate the "-subclusters.observations.txt" file which is spot id by genes CNVs I'm assuming?

Best wishes, Constantinos

xzz-1995 commented 1 week ago

Hello, thank you for your advice. I choose random_trees because it will give the most sensitive result that will differ spots belong to different CNV status. I'll add the 'leiden' as an option in the script for users who want to get results faster. Thank you.