qmtools

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see qmtools.

Quantitative Metabolomics Data Processing Tools

Bioconductor version: 3.21

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")):

Installation

To install this package, start R (version "4.5") and enter:


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

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("qmtools")

Quantitative metabolomics data processing HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DimensionReduction, MassSpectrometry, Metabolomics, Normalization, Preprocessing, Software

Version 1.12.0

In Bioconductor since BioC 3.15 (R-4.2) (3.5 years)

License GPL-3

Depends R (>= 4.2.0), SummarizedExperiment

Imports rlang, ggplot2, patchwork, heatmaply, methods, MsCoreUtils, stats, igraph, VIM, scales, grDevices, graphics, limma

System Requirements

URL https://github.com/HimesGroup/qmtools

Bug Reports https://github.com/HimesGroup/qmtools/issues

Suggests Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute, imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown

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Package Archives

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

Source Package qmtools_1.12.0.tar.gz

Windows Binary (x86_64) qmtools_1.12.0.zip

macOS Binary (x86_64) qmtools_1.12.0.tgz

macOS Binary (arm64) qmtools_1.12.0.tgz

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

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

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

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

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