qmtools

This is the development version of qmtools; for the stable release version, see qmtools.

Quantitative Metabolomics Data Processing Tools

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	1.11.0
In Bioconductor since	BioC 3.15 (R-4.2) (2.5 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
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report

Package Archives

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

Source Package	qmtools_1.11.0.tar.gz
Windows Binary (x86_64)	qmtools_1.11.0.zip
macOS Binary (x86_64)	qmtools_1.11.0.tgz
macOS Binary (arm64)	qmtools_1.11.0.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/
Package Downloads Report	Download Stats