Calculating Branch-specific gain rate and Branch-specific loss rate

[mapo121]

I have been going through the documentation on scMTNI. Currently, I am working on a project that requires me to study the cell states in the dentate gyrus.

However, I don't know how one would calculate the

• Branch-specific gain rate (The probability that an edge is gained in a child given that the edge is absent in the predecessor cell)
• Branch-specific loss rate (The probability that an edge is lost in a child given that the edge is present in the predecessor cell)

I'm assuming that one would look in the literature of some paper. Most of the papers I've been reading have been more about hematopoiesis; I'm interested in brain cells. Monocle2 had something similar (it's a cell trajectory tool). Would you know any existing tools that would output the tree that you describe in the section labeled: Prepare Cell Lineage Tree?

I really appreciate all the help - I'm learning a lot.

[mapo121]

I used a library that calculated the RNA velocity to give me the branch probabilities and the cell lineage tree. https://scvelo.readthedocs.io/en/stable/VelocityBasics.html#PAGA-velocity-graph

This example was using pancreatic cells - I used my brain data to draw out the lineage.

You have to use a library called velocityto before running scVelo.

https://velocyto.org/velocyto.py/index.html

Taken from: https://scvelo.readthedocs.io/en/stable/VelocityBasics.html#PAGA-velocity-graph

[mapo121]

https://docs.scipy.org/doc/scipy/reference/sparse.csgraph.html