pyseer 1.3.11-foss-2022a

Deprecated: Use of this version of pyseer is deprecated. More information on our Applications Support and Retention Policy.

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 pyseer/1.3.11-foss-2022a

BEAR Apps Version

2018b

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