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("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")| Quantitative metabolomics data processing | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, MassSpectrometry, Metabolomics, Normalization, Preprocessing, Software |
| Version | 1.2.0 |
| 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 |
| System Requirements | |
| URL | https://github.com/HimesGroup/qmtools |
| Bug Reports | https://github.com/HimesGroup/qmtools/issues |
See More
| Suggests | limma, 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_1.2.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |