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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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How to get the info in Table S1 #340

Closed pigraul closed 2 years ago

pigraul commented 2 years ago

Hi Dr qiu,

How can I get effector-regulator pairs cross cell types？ I tried dynamo.vf.rank_jacobian_genes(mode='int') , it generated pairs in each cell type.

Thank you!

Xiaojieqiu commented 2 years ago

Hey @pigraul there is an argument return_df for all dyn.vf.rank_* functions. you can set it to be True to return the ranking information.

dummyindex commented 2 years ago

https://dynamo-release.readthedocs.io/en/latest/_autosummary/dynamo.vf.rank_jacobian_genes.html#dynamo.vf.rank_jacobian_genes

pigraul commented 2 years ago

Thanks @Xiaojieqiu and @dummyindex .

I noticed the table header "Mono_baso_curv". Dose it mean I should compute the cell curvature and set a cutoff vaule to defind the cell is bifurcation or not. If not, in which way I can compute the cell fate bifurcation?

Xiaojieqiu commented 2 years ago

You need to manually select cells near the bifurcation point and then define those cells as Mono_baso or the like. Then you can perform differential geometry analyses for those cells.