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wgzgithub / VeTra

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Parameter optimalization #2

Open EmilyMiddendorp opened 3 years ago

EmilyMiddendorp commented 3 years ago

Hi! I am using VeTra to make a TI analysis on my dataset and just read the new version of the paper. I was wondering when will the GitHub be updated on how to identify the influential transcription factors? Also I am trying different parameters to identify the appropriate paths of my dataset, do you have any tips on how to choose the appropriate WCC and k parameters?

Thank you so much for the great package!

wgzgithub commented 3 years ago

Thanks for your interest. We are going to update new version recently. Based on my experience, 30-50 wcc is good for the number of cells smaller than 5000. If there are many strange velocities in your datasets, you should also change the parameter "deltathreshold". ( in new version, deltaThreshold is adjustable)

EmilyMiddendorp commented 3 years ago

Thanks for your interest. We are going to update new version recently. Based on my experience, 30-50 wcc is good for the number of cells smaller than 5000. If there are many strange velocities in your datasets, you should also change the parameter "deltathreshold". ( in new version, deltaThreshold is adjustable)

Thank you for your fast answer! I have a dataset with 40k cells and one dataset with 88 k cells. For the first dataset the parameters 15-30 worked quite well. However for the 88k cells I am having problems finding the right parameters.

I look forward to the update of the package!