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.
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).
Documentation
Important Notes
- 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
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 $SCVELO_SRC/tests/test_basic.py [user@cn0911 ~]$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'End the interactive session:
[user@cn0911 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$