SigProfilerMatrixGenerator 1.1.7-foss-2019b-Python-3.7.4

SigProfilerMatrixGenerator is a python framework that creates mutational matrices for somatic mutations. This tool works to identify and categorize the mutations based on possible single nucleotide variants (SNVs), double base substitutions (DBS), and insertions/deletions and provides further transcriptional strand bias categorization. It downsizes the generated mutations to parts of the genome like the exome or a custom BED file to help identify true mutational signatures within a genome. SigProfilerMatrixGenerator seamlessly integrates with other SigProfiler tools.

Accessing SigProfilerMatrixGenerator 1.1.7-foss-2019b-Python-3.7.4

To load the module for SigProfilerMatrixGenerator 1.1.7-foss-2019b-Python-3.7.4 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load SigProfilerMatrixGenerator/1.1.7-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.

Extensions

  • SigProfilerMatrixGenerator 1.1.7
  • sigProfilerPlotting 1.1.0

More Information

For more information visit the SigProfilerMatrixGenerator website.

Dependencies

This version of SigProfilerMatrixGenerator has a direct dependency on: foss/2019b matplotlib/3.1.1-foss-2019b-Python-3.7.4 Python/3.7.4-GCCcore-8.3.0 SciPy-bundle/2019.10-foss-2019b-Python-3.7.4 statsmodels/0.11.0-foss-2019b-Python-3.7.4

Required By

This version of SigProfilerMatrixGenerator is a direct dependent of: SigProfilerMatrixGeneratorR/1.1-foss-2019b-R-3.6.2-Python-3.7.4

Last modified on 6th March 2020