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.

References:

• Volker Bergen, Marius Lange, Stefan Peidli, F. Alexander Wolf and Fabian J. Theis
  Generalizing RNA velocity to transient cell states through dynamical modeling
  Nature Biotechnology 38, 1408-1414 (2020).

• scVelo GitHub page
• scVelo Documentation

• Module Name: scVelo (see the modules page for more information)
• Unusual environment variables set
  • SCVELO_HOME  installation directory
  • SCVELO_BIN       executable directory
  • SCVELO_SRC       source code directory
  • SCVELO_DATA  sample data directory

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 $SCVELO_SRC/tests/test_basic.py
[user@cn0911 ~]$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__
'0.52.0'

[user@cn0911 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$