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metapone

This is the development version of metapone; for the stable release version, see metapone.

Conducts pathway test of metabolomics data using a weighted permutation test

Bioconductor version: Development (3.18)

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 (from within R, enter citation("metapone")):

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF

Details

biocViews MassSpectrometry, Metabolomics, Pathways, Software, Technology
Version 1.7.0
In Bioconductor since BioC 3.14 (R-4.1) (2 years)
License Artistic-2.0
Depends R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea, ggplot2, ggrepel
Imports methods
Linking To
Suggests rmarkdown, knitr
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Enhances
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Package Archives

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

Source Package metapone_1.7.0.tar.gz
Windows Binary metapone_1.7.0.zip
macOS Binary (x86_64) metapone_1.7.0.tgz
macOS Binary (arm64) metapone_1.7.0.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