MWASTools
This is the released version of MWASTools; for the devel version, see MWASTools.
MWASTools: an integrated pipeline to perform metabolome-wide association studies
Bioconductor version: Release (3.23)
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("MWASTools")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.36.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 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 |
| 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_1.36.0.tar.gz |
| Windows Binary (x86_64) | MWASTools_1.36.0.zip |
| macOS Binary (big-sur-x86_64) | MWASTools_1.36.0.tgz |
| macOS Binary (sonoma-arm64) | MWASTools_1.36.0.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 |