Compass Advanced Usage Tutorial

Compass allows users to customize various features when using compass.

usage: compass [-h] --data FILE [--model MODEL] [--species SPECIES]
               [--media MEDIA] [--output-dir DIR] [--temp-dir DIR]
               [--torque-queue QUEUE] [--num-processes N] [--lambda F]
               [--num-threads N] [--and-function FXN] [--num-neighbors N]
               [--symmetric-kernel] [--input-weights FILE]
               [--penalty-diffusion MODE] [--no-reactions] [--no-metabolites]

Below we describe the features in more detail:

• and-function:
• input-weights:
• lambda: Smoothing factor for single-cell data. Should be set between 0 and 1
• media:
• model:
• no-metabolites:
• no-reactions:
• num-neighbors:
• num-processes: Number of processes for Compass to use. Ignored when submitting job onto a queue
• num-threads: Number of threads to use per sample. Default is 1
• output-dir:
• penalty-diffusion:
• species:
• symmetric-kernel:
• temp-dir:
• torque-queue: Name of the torque queue to submit to