qmtools
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see qmtools.
Quantitative Metabolomics Data Processing Tools
Bioconductor version: 3.17
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("qmtools")):
Installation
To install this package, start R (version "4.3") 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 | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, MassSpectrometry, Metabolomics, Normalization, Preprocessing, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2 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.
| Source Package | qmtools_1.4.0.tar.gz |
| Windows Binary | qmtools_1.4.0.zip |
| macOS Binary (x86_64) | qmtools_1.4.0.tgz |
| macOS Binary (arm64) | qmtools_1.4.0.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 |
| Old Source Packages for BioC 3.17 | Source Archive |