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Bioconductor - qmtools

qmtools

This is the released version of qmtools; for the devel version, see qmtools.

Quantitative Metabolomics Data Processing Tools

Bioconductor version: Release (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")
Details biocViews DimensionReduction, MassSpectrometry, Metabolomics, Normalization, Preprocessing, Software Version 1.12.0 In Bioconductor since BioC 3.15 (R-4.2) (3 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 See More Suggests Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute, imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown 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.

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