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metabCombiner

Method for Combining LC-MS Metabolomics Feature Measurements


Bioconductor version: Release (3.18)

This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Peak-picked and simply aligned metabolomics feature tables (consisting of m/z, rt, and per-sample abundance measurements, plus optional identifiers & adduct annotations) are accepted as input. The package outputs a combined table of feature pair alignments, organized into groups of similar m/z, and ranked by a similarity score. Input tables are assumed to be acquired using similar (but not necessarily identical) analytical methods.

Author: Hani Habra [aut, cre], Alla Karnovsky [ths]

Maintainer: Hani Habra <hhabra1 at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("metabCombiner")

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("metabCombiner")
Combine LC-MS Metabolomics Datasets with metabCombiner HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews MassSpectrometry, Metabolomics, Software
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.0)
Imports dplyr (>= 1.0), methods, mgcv, caret, S4Vectors, stats, utils, rlang, graphics, matrixStats, tidyr
System Requirements
URL
Bug Reports https://www.github.com/hhabra/metabCombiner/issues
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Suggests knitr, rmarkdown, testthat, BiocStyle
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Package Archives

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

Source Package metabCombiner_1.12.0.tar.gz
Windows Binary metabCombiner_1.12.0.zip
macOS Binary (x86_64) metabCombiner_1.12.0.tgz
macOS Binary (arm64) metabCombiner_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/metabCombiner
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/metabCombiner
Bioc Package Browser https://code.bioconductor.org/browse/metabCombiner/
Package Short Url https://bioconductor.org/packages/metabCombiner/
Package Downloads Report Download Stats