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aristoteleo / dynamo-release

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
https://dynamo-release.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Measure the impact of "Perturbation" #491

Closed Juneil-Jang closed 1 year ago

Juneil-Jang commented 1 year ago

Hi, I appreciate the good tool. I want to quantify the impact of perturbation of the in silico perturbed data. This package have that kind of analysis tool? if not, I wonder where I can find the estimated expression level by in silico perturbation. Thank you!

Xiaojieqiu commented 1 year ago

I am busy with several commitments this week and don't have the time to give you a detailed answer. However, you should read the method section regarding the in silico perturbation in our publication (https://www.sciencedirect.com/science/article/pii/S0092867421015774) and the following pages in our readthedocs to have a deep understanding of our approach:

the theory: https://dynamo-release.readthedocs.io/en/latest/notebooks/perturbation_introduction_theory.html the documentation of the perturbation function: https://dynamo-release.readthedocs.io/en/latest/_autosummary/dynamo.pd.perturbation.html#dynamo.pd.perturbation some examples on using it: https://dynamo-release.readthedocs.io/en/latest/notebooks/perturbation_tutorial/perturbation_tutorial.html

the newly generated j_delta_x_perturbation layer after running the perturbation predictions offers the perturbation effects of each gene in each gene. The values in this matrix quantify the impact of perturbation.