MWASTools
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MWASTools.
MWASTools: an integrated pipeline to perform metabolome-wide association studies
Bioconductor version: 3.10
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 <r.ayala14 at imperial.ac.uk>
citation("MWASTools")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Cheminformatics, Lipidomics, Metabolomics, QualityControl, Software, SystemsBiology |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 years) |
| License | CC BY-NC-ND 4.0 |
| Depends | R (>= 3.4) |
| Imports | glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra, igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST, ComplexHeatmap, stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | MetaboSignal |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MWASTools_1.10.0.tar.gz |
| Windows Binary | MWASTools_1.10.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | MWASTools_1.10.0.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 |
| Old Source Packages for BioC 3.10 | Source Archive |