Biowulf High Performance Computing at the NIH
scVelo: RNA velocity of single cell generalized through dynamical modeling.

scVelo is a method to describe the rate of gene expression change for an individual gene at a given time point based on the ratio of its spliced and unspliced messenger RNA (mRNA). It avoids errors in the velocity estimates by solving the full transcriptional dynamics of splicing kinetics using a likelihood-based dynamical model. This generalizes RNA velocity to systems with transient cell states, which are common in development and in response to perturbations.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=4g
[user@cn0911 ~]$module load scvelo  
[+] Loading scvelo  0.2.4  on cn0911
[+] Loading singularity  3.8.5  on cn0911
[user@cn0911 ~]$python $SCVELO_SRC/tests/
[user@cn0911 ~]$python 
Python 3.8.12 (default, Oct 12 2021, 13:49:34)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scvelo
>>> import numba
>>> numba.__version__
End the interactive session:
[user@cn0911 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$