RmzTabM
This is the development version of RmzTabM; to use it, please install the devel version of Bioconductor.
R API for the mzTab-M Reference Implementation
Bioconductor version: Development (3.24)
The RmzTabM package provides functions to read and write files in the HUPO-PSI mzTab-M file format for reporting of results from metabolomics and lipidomics experiments. This package represents the reference implementation for mzTab-M import/export for R. Core, low level functions allow to format and parse the individual sections of the mzTab-M format. These functions are designed to be re-used by other packages implementing import/export of results in mzTab-M.
Author: Nils Hoffmann [ctb]
, Steffen Neumann [ctb]
, Johannes Rainer [aut, cre]
, Philippine Louail [aut] (ORCID:
, fnd: European Union HORIZON-MSCA-2021 project Grant No. 101073062: HUMAN – Harmonising and Unifying Blood Metabolic Analysis Networks), Gabriele Tomè [aut] (ORCID:
, fnd: MetaRbolomics4Galaxy project (CUP: D53C25001030003) co-funded by the Autonomous Province of Bolzano under the Joint Projects South Tyrol–Germany 2025 program.)
Maintainer: Johannes Rainer <johannes.rainer at eurac.edu>
citation("RmzTabM")):
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("RmzTabM")
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("RmzTabM")| rmztabm-api.html | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.6) |
| Imports | data.table, methods, SummarizedExperiment, stats, utils |
| System Requirements | pandoc, quarto |
| URL | https://github.com/RforMassSpectrometry/RmzTabM |
| Bug Reports | https://github.com/RforMassSpectrometry/RmzTabM/issues |
See More
| Suggests | testthat, pkgdown, BiocStyle, knitr, rmarkdown, quarto, pander |
| 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 | RmzTabM_0.99.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | RmzTabM_0.99.1.tgz |
| macOS Binary (sonoma-arm64) | RmzTabM_0.99.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RmzTabM |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RmzTabM |
| Bioc Package Browser | https://code.bioconductor.org/browse/RmzTabM/ |
| Package Short Url | https://bioconductor.org/packages/RmzTabM/ |
| Package Downloads Report | Download Stats |