structToolbox

DOI: 10.18129/B9.bioc.structToolbox    

Data processing & analysis tools for Metabolomics and other omics

Bioconductor version: Release (3.14)

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.

Author: Gavin Rhys Lloyd [aut, cre], Ralf Johannes Maria Weber [aut]

Maintainer: Gavin Rhys Lloyd <g.r.lloyd at bham.ac.uk>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("structToolbox")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("structToolbox")

 

HTML	R Script	Data analysis of metabolomics and other omics datasets using the structToolbox
PDF		Reference Manual
Text		NEWS

Details

biocViews	Metabolomics, Software, WorkflowStep
Version	1.6.1
In Bioconductor since	BioC 3.11 (R-4.0) (2 years)
License	GPL-3
Depends	R (>= 4.0), struct(>= 1.5.1)
Imports	ggplot2, ggthemes, grid, gridExtra, methods, scales, sp, stats, utils
LinkingTo
Suggests	agricolae, BiocFileCache, BiocStyle, car, covr, cowplot, e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls, pmp, reshape2, ropls, rmarkdown, Rtsne, testthat, rappdirs
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	metabolomicsWorkbenchR
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	structToolbox_1.6.1.tar.gz
Windows Binary	structToolbox_1.6.1.zip
macOS 10.13 (High Sierra)	structToolbox_1.6.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/structToolbox
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/structToolbox
Package Short Url	https://bioconductor.org/packages/structToolbox/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive