scirpy
Link to section 'Introduction' of 'scirpy' Introduction
Scirpy is a scalable python-toolkit to analyse T cell receptor (TCR) or B cell receptor (BCR) repertoires from single-cell RNA sequencing (scRNA-seq) data. It seamlessly integrates with the popular scanpy library and provides various modules for data import, analysis and visualization.
Home page: https://github.com/scverse/scirpy
Link to section 'Versions' of 'scirpy' Versions
- 0.10.1
Link to section 'Commands' of 'scirpy' Commands
- python
- python3
Link to section 'Module' of 'scirpy' Module
You can load the modules by:
module load biocontainers
module load scirpy
Link to section 'Example job' of 'scirpy' Example 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 run scirpy on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=scirpy
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers scirpy