This repo is deprecated. Please check out our more updated tutorial repos here. Also I suggest dynamo users to go through our readthedocs pages to help you get started: this includes the Introduction, 10 minutes to dynamo, API, tutorials on how to analyzing conventional scRNA-seq and tutorials on analyzing both scNT-seq, scEU-seq datasets, etc. (those tutorials are also in the updated tutorial repo)
Tutorials of Dynamo usage cases and code to reproduce the manuscript.
This is our inital release of dynamo related notebooks (as of July 9, 2019). More detailed tutorials on velocity estimation for scSLAM-seq (protein / RNA coassay) data, functional vector field reconstruction, global mapping of potential landscape will be released in a couple days.
It is brought to our attention that we didn't refer the package version we used in Figure 1. We used scvelo version 0.1.18 and velocyto 0.17.13 in our Gillespie simulation benchmark. We also note that dynamo benefits from real time information in this benchmark while the other two tools don't rely on this information. Note that now we are also releasing the full derivation of the matrix form of the moment generation functions for parameter estimation in full_derivation.pdf file.