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MWASTools

MWASTools: an integrated pipeline to perform metabolome-wide association studies

Bioconductor version: Release (3.17)

MWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.

Author: Andrea Rodriguez-Martinez, Joram M. Posma, Rafael Ayala, Ana L. Neves, Maryam Anwar, Jeremy K. Nicholson, Marc-Emmanuel Dumas

Maintainer: Andrea Rodriguez-Martinez <andrea.rodriguez-martinez13 at imperial.ac.uk>, Rafael Ayala <rafael.ayala at oist.jp>

Citation (from within R, enter citation("MWASTools")):

Installation

To install this package, start R (version "4.3") and enter: 

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

BiocManager::install("MWASTools")

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("MWASTools")
MWASTools HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Cheminformatics, Lipidomics, Metabolomics, QualityControl, Software, SystemsBiology
Version 1.24.0
In Bioconductor since BioC 3.5 (R-3.4) (6.5 years)
License CC BY-NC-ND 4.0
Depends R (>= 3.5.0)
Imports glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra, igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST, ComplexHeatmap, stats, utils
Linking To
Suggests RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me MetaboSignal
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package MWASTools_1.24.0.tar.gz
Windows Binary MWASTools_1.24.0.zip
macOS Binary (x86_64) MWASTools_1.24.0.tgz
macOS Binary (arm64) MWASTools_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MWASTools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MWASTools
Bioc Package Browser https://code.bioconductor.org/browse/MWASTools/
Package Short Url https://bioconductor.org/packages/MWASTools/
Package Downloads Report Download Stats