This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see qmtools.
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")
):
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.
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 |
Reference Manual | ||
Text | NEWS |
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 |
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 |
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