celltypist
Link to section 'Introduction' of 'celltypist' Introduction
Celltypist
is a tool for semi-automatic cell type annotation.
For more information, please check its website: https://biocontainers.pro/tools/celltypist and its home page on Github.
Link to section 'Versions' of 'celltypist' Versions
- 0.2.0
- 1.1.0
Link to section 'Commands' of 'celltypist' Commands
- celltypist
- python
- python3
Link to section 'Module' of 'celltypist' Module
You can load the modules by:
module load biocontainers
module load celltypist
Link to section 'Example job' of 'celltypist' 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 Celltypist on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=celltypist
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers celltypist
celltypist --indata demo_2000_cells.h5ad --model Immune_All_Low.pkl --outdir output