MetMashR

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see MetMashR.

Metabolite Mashing with R

Bioconductor version: 3.20

A package to merge, filter sort, organise and otherwise mash together metabolite annotation tables. Metabolite annotations can be imported from multiple sources (software) and combined using workflow steps based on S4 class templates derived from the `struct` package. Other modular workflow steps such as filtering, merging, splitting, normalisation and rest-api queries are included.

Author: Gavin Rhys Lloyd [aut, cre] ORCID iD ORCID: 0000-0001-7989-6695 , Ralf Johannes Maria Weber [aut]

Maintainer: Gavin Rhys Lloyd <g.r.lloyd at bham.ac.uk>

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

Installation

To install this package, start R (version "4.4") and enter:


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

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("MetMashR")

Annotation of mixtures of standards HTML R Script

Exploring the MTox700+ library HTML R Script

Extending MetMashR HTML R Script

Using MetMashR HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews KEGG, Metabolomics, Software, WorkflowStep

Version 1.0.0

In Bioconductor since BioC 3.20 (R-4.4) (< 6 months)

License GPL-3

Depends R (>= 4.3.0), struct

Imports dplyr, methods, httr, scales, ggthemes, ggplot2, utils, rlang, cowplot, stats

System Requirements

URL https://computational-metabolomics.github.io/MetMashR/

Bug Reports https://github.com/computational-metabolomics/MetMashR/issues

Suggests covr, httptest, knitr, rmarkdown, testthat (>= 3.0.0), rgoslin, DT, RSQLite, CompoundDb, BiocStyle, BiocFileCache, msPurity, ChemmineOB, rsvg, metabolomicsWorkbenchR, KEGGREST, plyr, magick, structToolbox, RVenn, ggVennDiagram, patchwork, XML, GO.db, tidytext, tidyr, tidyselect, ComplexUpset, jsonlite, openxlsx

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 MetMashR_1.0.0.tar.gz

Windows Binary (x86_64) MetMashR_1.0.0.zip

macOS Binary (x86_64) MetMashR_1.0.0.tgz

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/MetMashR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MetMashR

Bioc Package Browser https://code.bioconductor.org/browse/MetMashR/

Package Short Url https://bioconductor.org/packages/MetMashR/

Package Downloads Report Download Stats