LEfSe 1.1-foss-2019b-Python-3.7.4

LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.

Accessing LEfSe 1.1-foss-2019b-Python-3.7.4

To load the module for LEfSe 1.1-foss-2019b-Python-3.7.4 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load LEfSe/1.1-foss-2019b-Python-3.7.4

BEAR Apps Version

2019b

Architectures

EL8-cascadelake — EL8-haswell — Ubuntu20.04-haswell

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.

More Information

For more information visit the LEfSe website.

Dependencies

This version of LEfSe has a direct dependency on: biom-format/2.1.8-foss-2019b-Python-3.7.4 foss/2019b matplotlib/3.1.1-foss-2019b-Python-3.7.4 Python/3.7.4-GCCcore-8.3.0 R/3.6.2-foss-2019b rpy2/3.2.6-foss-2019b-Python-3.7.4 SciPy-bundle/2019.10-foss-2019b-Python-3.7.4

Last modified on 25th September 2020