Compass 20220402-foss-2020b

Compass is an algorithm to characterize the metabolic state of cells based on single-cell RNA-Seq and flux balance analysis (FBA). Its development was motivated by the challenge in characterizing the metabolic states of single cells on scale with current metabolic assays. Compass is an in silico approach to infer metabolic status of cells based on transcriptome data, which is readily available even in single cell resolutions. For a detailed description of the algorithm, refer to Wagner et al., Cell 2021

Accessing Compass 20220402-foss-2020b

To load the module for Compass 20220402-foss-2020b please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load Compass/20220402-foss-2020b

BEAR Apps Version




The listed architectures consist of two part: OS-CPU.

  • BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
  • BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.


  • anndata 0.7.6
  • Compass 20220402
  • natsort 7.1.1
  • python_libsbml 5.19.7

More Information

For more information visit the Compass website.


This version of Compass has a direct dependency on: CPLEX/20.10-GCCcore-10.2.0 foss/2020b h5py/3.1.0-foss-2020b leidenalg/0.8.3-foss-2020b Python/3.8.6-GCCcore-10.2.0 python-igraph/0.9.0-foss-2020b scikit-learn/0.23.2-foss-2020b SciPy-bundle/2020.11-foss-2020b tqdm/4.56.2-GCCcore-10.2.0

Last modified on 26th October 2022