structToolbox
This is the development version of structToolbox; for the stable release version, see structToolbox.
Data processing & analysis tools for Metabolomics and other omics
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Gavin Rhys Lloyd <g.r.lloyd at bham.ac.uk>
citation("structToolbox")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")| Data analysis of metabolomics and other omics datasets using the structToolbox | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Metabolomics, Software, WorkflowStep |
| Version | 1.19.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.0), struct(>= 1.5.1) |
| Imports | ggplot2, ggthemes, grid, gridExtra, methods, scales, sp, stats |
| System Requirements | |
| URL | https://github.com/computational-metabolomics/structToolbox https://computational-metabolomics.github.io/structToolbox/ |
See More
| Suggests | agricolae, BiocFileCache, BiocStyle, car, covr, cowplot, e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls, pmp, reshape2, ropls, rmarkdown, Rtsne, testthat, rappdirs |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | MetMashR, metabolomicsWorkbenchR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | structToolbox_1.19.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/structToolbox |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/structToolbox |
| Bioc Package Browser | https://code.bioconductor.org/browse/structToolbox/ |
| Package Short Url | https://bioconductor.org/packages/structToolbox/ |
| Package Downloads Report | Download Stats |