metapone
Conducts pathway test of metabolomics data using a weighted permutation test
Bioconductor version: Release (3.20)
The package conducts pathway testing from untargetted metabolomics data. It requires the user to supply feature-level test results, from case-control testing, regression, or other suitable feature-level tests for the study design. Weights are given to metabolic features based on how many metabolites they could potentially match to. The package can combine positive and negative mode results in pathway tests.
Author: Leqi Tian [aut], Tianwei Yu [aut], Tianwei Yu [cre]
Maintainer: Tianwei Yu <yutianwei at cuhk.edu.cn>
citation("metapone")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("metapone")
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("metapone")| metapone | HTML | R Script |
| Reference Manual |
Details
| biocViews | MassSpectrometry, Metabolomics, Pathways, Software, Technology |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea, ggplot2, ggrepel |
| Imports | methods |
| System Requirements | |
| URL |
See More
| Suggests | rmarkdown, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | metapone_1.12.0.tar.gz |
| Windows Binary (x86_64) | metapone_1.12.0.zip |
| macOS Binary (x86_64) | metapone_1.12.0.tgz |
| macOS Binary (arm64) | metapone_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/metapone |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/metapone |
| Bioc Package Browser | https://code.bioconductor.org/browse/metapone/ |
| Package Short Url | https://bioconductor.org/packages/metapone/ |
| Package Downloads Report | Download Stats |