Introduction a library for the analysis of RNA velocity.

Detailed information about can be found here:


  • 0.17.17


  • python

  • python3

  • velocyto


You can load the modules by:

module load biocontainers
module load

Interactive job

To run interactively on our clusters:

(base) UserID@bell-fe00:~ $ sinteractive -N1 -n12 -t4:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers cellrank/1.5.1
(base) UserID@bell-a008:~ $ python
Python 3.9.10 |  packaged by conda-forge |  (main, Feb  1 2022, 21:24:11)
[GCC 9.4.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import velocyto as vcy
>>> vlm = vcy.VelocytoLoom("YourData.loom")
>>> vlm.normalize("S", size=True, log=True)
>>> vlm.S_norm  # contains log normalized

Batch job


Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To submit a sbatch job on our clusters:

#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -n 24
#SBATCH --job-name=Velocyto
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers

velocyto run10x cellranger_count_1kpbmcs_out refdata-gex-GRCh38-2020-A/genes/genes.gtf