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https://github.com/bioconductor-source/structtoolbox

https://github.com/bioconductor-source/structtoolbox

Science Score: 13.0%

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Repository

Basic Info
  • Host: GitHub
  • Owner: bioconductor-source
  • License: gpl-3.0
  • Language: R
  • Default Branch: devel
  • Size: 13.1 MB
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  • Stars: 0
  • Watchers: 2
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Created almost 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License

README.md

structToolbox

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.

Installation

To install this package:

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

BiocManager::install("structToolbox") ```

To install the development version:

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

remotes::install_github("computational-metabolomics/structToolbox") ```

BioC version BioC status <!-- badges: end -->

Owner

  • Name: (WIP DEV) Bioconductor Packages
  • Login: bioconductor-source
  • Kind: organization
  • Email: maintainer@bioconductor.org

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Dependencies

.github/workflows/check-bioc.yml actions
  • JamesIves/github-pages-deploy-action releases/v4 composite
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v4 composite
  • docker/login-action v2 composite
  • docker/setup-buildx-action v2 composite
  • docker/setup-qemu-action v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
DESCRIPTION cran
  • R >= 4.0 depends
  • struct >= 1.5.1 depends
  • ggplot2 * imports
  • ggthemes * imports
  • grid * imports
  • gridExtra * imports
  • methods * imports
  • scales * imports
  • sp * imports
  • stats * imports
  • BiocFileCache * suggests
  • BiocStyle * suggests
  • Rtsne * suggests
  • agricolae * suggests
  • car * suggests
  • covr * suggests
  • cowplot * suggests
  • e1071 * suggests
  • emmeans * suggests
  • ggdendro * suggests
  • knitr * suggests
  • magick * suggests
  • nlme * suggests
  • openxlsx * suggests
  • pls * suggests
  • pmp * suggests
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  • reshape2 * suggests
  • rmarkdown * suggests
  • ropls * suggests
  • testthat * suggests