loomsampler

A straightforward script to randomly sample items (usually cells) from a loom file.

Python environment requirements

A Conda environment file can be found here: src/env.yml

Slurm compatible bash launcher

The script can be launched using Slurm:

sbatch launcher.sh

Representativity

A minimum number of items can be passed to the script with the -m, --minimum option. Default value is 10.

For a given combination, if a number of items lower than this minimum value were to be sampled, use the minimum value instead, or as many items as possible if there are less items available.