This repo hosts scripts of OTVelo, a software for gene regulatory network inference from time-stamped gene expresssion matrices. Paper link: https://www.biorxiv.org/content/10.1101/2024.09.12.612590v1
We introduce a framework for inferring the gene regulatory network (GRN) from time-stamped data. First, trajectory inference is performed through fused Gromov-Wasserstein, and velocities of evolution is inferred based on the coupling matrices. Finally, we can infer the GRN based on either (1) OTVelo-Corr
the correlation between velocities, or (2) OTVelo-Granger
Granger causality between velocities.
An example for demonstration can be found from Tutorial.ipynb
. It provides details for running the algorithm, visualizing the resulting vector field and graphs, as well as computations of metrics.
Run pip3 install -r requirements.txt
to install all the required packages.
The scripts reproducing the examples on simulations can be found from Scripts
. To reproduce the experiments from HARISSA
simulations, use the script Harissa-myVelo.ipynb
. To reproduce the experiments from curated networks, use the script Curated-myVelo.ipynb
. Note that datasets need to be downloaded from their associated publications, and instructions are inserted in the two notebooks as mentioned.
Similarly, a notebook reproducing the results for a real data is provided as Scripts/Kouno-myVelo.ipynb
. Note that the original data will need to be downloaded from https://github.com/CABSEL/SINCERITIES.