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structToolbox

R/Bioconductor package - STRUCT (STatistics in R Using Class Templates) Toolbox: An extensive set of data (pre-)processing and analysis methods and tools for metabolomics and other omics,

https://github.com/computational-metabolomics/structtoolbox

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    DOI references
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    Academic publication links
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    Committers with academic emails
    3 of 7 committers (42.9%) from academic institutions
  • ○
    Institutional organization owner
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (10.5%) to scientific vocabulary

Keywords

bioconductor-package dims lc-ms machine-learning metabolomics multivariate-analysis r-package statistics univariate

Keywords from Contributors

sequencing immune-repertoire gene grna-sequence genomics ontology transcriptomics proteomics mass-spectrometry bioinformatics
Last synced: 6 months ago · JSON representation

Repository

R/Bioconductor package - STRUCT (STatistics in R Using Class Templates) Toolbox: An extensive set of data (pre-)processing and analysis methods and tools for metabolomics and other omics,

Basic Info
Statistics
  • Stars: 10
  • Watchers: 4
  • Forks: 4
  • Open Issues: 10
  • Releases: 21
Topics
bioconductor-package dims lc-ms machine-learning metabolomics multivariate-analysis r-package statistics univariate
Created almost 7 years ago · Last pushed 9 months 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: Computational Metabolomics Research Group
  • Login: computational-metabolomics
  • Kind: organization
  • Email: r.j.weber@bham.ac.uk
  • Location: University of Birmingham, United Kingdom

GitHub Events

Total
  • Watch event: 1
  • Push event: 4
  • Create event: 3
Last Year
  • Watch event: 1
  • Push event: 4
  • Create event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 455
  • Total Committers: 7
  • Avg Commits per committer: 65.0
  • Development Distribution Score (DDS): 0.246
Past Year
  • Commits: 31
  • Committers: 3
  • Avg Commits per committer: 10.333
  • Development Distribution Score (DDS): 0.129
Top Committers
Name Email Commits
grlloyd g****d@b****k 343
Gavin Rhys Lloyd g****d 78
Ralf Weber R****W 17
Nitesh Turaga n****a@g****m 10
RJMW r****r@b****k 3
J Wokaty j****y@s****u 2
J Wokaty j****y 2
Committer Domains (Top 20 + Academic)
bham.ac.uk: 2 sph.cuny.edu: 1

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 12,188 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
bioconductor.org: structToolbox

Data processing & analysis tools for Metabolomics and other omics

  • Versions: 7
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 12,188 Total
Rankings
Dependent repos count: 0.0%
Forks count: 5.1%
Stargazers count: 12.3%
Dependent packages count: 19.9%
Average: 21.6%
Downloads: 70.6%
Maintainers (1)
g.r.lloyd@bham.ac.uk
Last synced: 6 months ago

Dependencies

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
  • utils * 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
  • rappdirs * suggests
  • reshape2 * suggests
  • rmarkdown * suggests
  • ropls * suggests
  • testthat * suggests
.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 v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite