MetMashR
This is the development version of MetMashR; for the stable release version, see MetMashR.
Metabolite Mashing with R
Bioconductor version: Development (3.24)
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]
, Ralf Johannes Maria Weber [aut]
Maintainer: Gavin Rhys Lloyd <g.r.lloyd at bham.ac.uk>
citation("MetMashR")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | ||
| NEWS | Text |
Details
| biocViews | KEGG, Metabolomics, Software, WorkflowStep |
| Version | 1.7.1 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | GPL-3 |
| Depends | R (>= 4.3.0), struct |
| Imports | dplyr, methods, httr, scales, ggthemes, utils, rlang, stats, ggplot2 |
| System Requirements | |
| URL | https://computational-metabolomics.github.io/MetMashR/ |
| Bug Reports | https://github.com/computational-metabolomics/MetMashR/issues |
See More
| Suggests | covr, httptest, knitr, rmarkdown, testthat (>= 3.0.0), rgoslin, DT, RSQLite, CompoundDb, BiocStyle, BiocFileCache, msPurity, rsvg, metabolomicsWorkbenchR, KEGGREST, plyr, magick, structToolbox, ggVennDiagram, patchwork, XML, GO.db, tidytext, tidyr, tidyselect, ComplexUpset, jsonlite, openxlsx, ggplotify, cowplot |
| 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_1.7.1.tar.gz |
| Windows Binary (x86_64) | MetMashR_1.7.0.zip |
| macOS Binary (big-sur-x86_64) | MetMashR_1.7.1.tgz |
| macOS Binary (sonoma-arm64) | MetMashR_1.7.0.tgz |
| 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 |