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Roy-lab / scMTNI

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Running scMTNI with subsampling #13

Closed PeterZZQ closed 2 months ago

PeterZZQ commented 9 months ago

Hi,

I tried to improve the inference accuracy by generating the subsample of the original dataset. I generated a subsample with the command

python Scripts/Datasubsample_sc_merged.py --filelist $filelist --indir $indir --nseed 100

but there is no guidance on how to run scMTNI afterwards. Am I supposed to run scMTNI one by one for each subsampled dataset?

shiluzhang commented 8 months ago

Hi Peter, Thank you for your interest in scMTNI. Yes, you can run scMTNI one by one for each subsampled dataset using the code in Step 3: https://github.com/Roy-lab/scMTNI#step-3-run. After all the subsamples' networks are generated, you can use this script to create consensus networks across subsamples: https://github.com/Roy-lab/scMTNI#40-generate-consensus-network-for-subsample-results Please let us know if you have more questions.

Best, Shilu