structToolbox 1.0.1-foss-2020a-R-4.0.0

An extensive set of data (pre-)processing and analysis methods and tools for metabolomics and other omics, with a strong emphasis on statistics and machine learning. This toolbox allows the user to build extensive and standardised workflows for data analysis. The methods and tools have been implemented using class-based templates provided by the struct (Statistics in R Using Class-based Templates) package. The toolbox includes pre-processing methods (e.g. signal drift and batch correction, normalisation, missing value imputation and scaling), univariate (e.g. ttest, various forms of ANOVA, Kruskal–Wallis test and more) and multivariate statistical methods (e.g. PCA and PLS, including cross-validation and permutation testing) as well as machine learning methods (e.g. Support Vector Machines). The STATistics Ontology (STATO) has been integrated and implemented to provide standardised definitions for the different methods, inputs and outputs.

Accessing structToolbox 1.0.1-foss-2020a-R-4.0.0

To load the module for structToolbox 1.0.1-foss-2020a-R-4.0.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load structToolbox/1.0.1-foss-2020a-R-4.0.0

BEAR Apps Version

2020a

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

  • agricolae-1.3-3
  • BiocStyle 2.16.1
  • bookdown 0.21
  • emmeans 1.5.3
  • estimability 1.3
  • ggdendro 0.1.22
  • ggthemes 4.2.4
  • knitr 1.30
  • MultiDataSet 1.16.0
  • ontologyIndex 2.5
  • pmp 1.0.0
  • qqman 0.1.4
  • ropls 1.20.0
  • struct 1.0.0
  • structToolbox 1.0.1
  • xfun 0.20

More Information

For more information visit the structToolbox website.

Dependencies

This version of structToolbox has a direct dependency on: foss/2020a R/4.0.0-foss-2020a R-bundle-Bioconductor/3.11-foss-2020a-R-4.0.0

Required By

This version of structToolbox is a direct dependent of: BEAR-R-bio/2020a-foss-2020a-R-4.0.0

Last modified on 26th January 2021