qmtools
This is the development version of qmtools; for the stable release version, see qmtools.
All Bioconductor versions of qmtools
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15
Quantitative Metabolomics Data Processing Tools
Bioconductor version: 3.24 · Package version: 1.17.0
The qmtools (quantitative metabolomics tools) package provides basic tools for processing quantitative metabolomics data with the standard SummarizedExperiment class. This includes functions for imputation, normalization, feature filtering, feature clustering, dimension-reduction, and visualization to help users prepare data for statistical analysis. This package also offers a convenient way to compute empirical Bayes statistics for which metabolic features are different between two sets of study samples. Several functions in this package could also be used in other types of omics data.
Author: Jaehyun Joo [aut, cre], Blanca Himes [aut]
Maintainer: Jaehyun Joo <jaehyunjoo at outlook.com>
Citation
From within R, enter citation("qmtools"):
Jaehyun Joo, Blanca Himes. qmtools: Quantitative Metabolomics Data Processing Tools. doi:10.18129/B9.bioc.qmtools, R package version 1.17.0, https://bioconductor.org/packages/qmtools.
Generated from the package metadata; it may differ from the package's own citation.
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("qmtools")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.17.0 |
| License | GPL-3 |
| URL | https://github.com/HimesGroup/qmtools |
| Bug Reports | https://github.com/HimesGroup/qmtools/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4 years) |
| Downloads rank | 1641 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DimensionReduction, MassSpectrometry, Metabolomics, Normalization, Preprocessing, Software |
| Package Short Url | https://bioconductor.org/packages/qmtools/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("qmtools")| Processing quantitative metabolomics data with the qmtools package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | qmtools_1.17.0.tar.gz |
| Windows binary (x86_64) | qmtools_1.17.0.zip |
| macOS binary (arm64) | qmtools_1.17.0.tgz |
| macOS binary (x86_64) | qmtools_1.17.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/qmtools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/qmtools |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.2.0), SummarizedExperiment
Imports: rlang, ggplot2, patchwork, heatmaply, methods, MsCoreUtils, stats, igraph, VIM, scales, grDevices, graphics, limma
Suggests: Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute, imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown