qmtools

DOI: 10.18129/B9.bioc.qmtools    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see qmtools.

Quantitative Metabolomics Data Processing Tools

Bioconductor version: 3.15

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. 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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Quantitative metabolomics data processing
PDF		Reference Manual
Text		NEWS

Details

biocViews	DimensionReduction, MassSpectrometry, Metabolomics, Normalization, Preprocessing, Software
Version	1.0.0
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 years)
License	GPL-3
Depends	R (>= 4.2.0), SummarizedExperiment
Imports	rlang, ggplot2, patchwork, heatmaply, methods, MsCoreUtils, stats, igraph, VIM, scales, grDevices, graphics
LinkingTo
Suggests	limma, Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute, imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/HimesGroup/qmtools
BugReports	https://github.com/HimesGroup/qmtools/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	qmtools_1.0.0.tar.gz
Windows Binary	qmtools_1.0.0.zip
macOS Binary (x86_64)	qmtools_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/qmtools
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/qmtools
Package Short Url	https://bioconductor.org/packages/qmtools/
Package Downloads Report	Download Stats