pyseer 1.3.11-foss-2022a

pyseer was first written a python reimplementation of seer, which was written in C++. pyseer uses linear models with fixed or mixed effects to estimate the effect of genetic variation in a bacterial population on a phenotype of interest, while accounting for potentially very strong confounding population structure. This allows for genome-wide association studies (GWAS) to be performed in clonal organisms such as bacteria and viruses.

Accessing pyseer 1.3.11-foss-2022a

To load the module for pyseer 1.3.11-foss-2022a please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load bear-apps/2022a
module load pyseer/1.3.11-foss-2022a

BEAR Apps Version

2022a

Architectures

EL8-cascadelake — EL8-haswell — EL8-icelake

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 Cloud and CaStLeS 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.

Extensions

  • glmnet-python-1.0.2
  • pyseer 1.3.11

More Information

For more information visit the pyseer website.

Dependencies

This version of pyseer has a direct dependency on: DendroPy/4.5.2-GCCcore-11.3.0 foss/2022a matplotlib/3.5.2-foss-2022a pybedtools/0.9.0-GCC-11.3.0 Pysam/0.19.1-GCC-11.3.0 Python/3.10.4-GCCcore-11.3.0 scikit-learn/1.1.2-foss-2022a SciPy-bundle/2022.05-foss-2022a statsmodels/0.13.1-foss-2022a tqdm/4.64.0-GCCcore-11.3.0

Last modified on 21st June 2023