qmtools

DOI: 10.18129/B9.bioc.qmtools  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see qmtools.

Quantitative Metabolomics Data Processing Tools

Bioconductor version: 3.16

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>

Citation (from within R, enter citation("qmtools")):

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 1.2.0
In Bioconductor since BioC 3.15 (R-4.2) (1 year)
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_1.2.0.tar.gz
Windows Binary qmtools_1.2.0.zip
macOS Binary (x86_64) qmtools_1.2.0.tgz
macOS Binary (arm64) qmtools_1.2.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: