metabCombiner

DOI: 10.18129/B9.bioc.metabCombiner    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see metabCombiner.

Method for Combining LC-MS Metabolomics Feature Measurements

Bioconductor version: 3.14

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>

Installation

To install this package, start R (version "4.1") 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")

 

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

Details

biocViews	MassSpectrometry, Metabolomics, Software
Version	1.4.0
In Bioconductor since	BioC 3.12 (R-4.0) (1.5 years)
License	GPL-3
Depends	R (>= 4.0), dplyr (>= 1.0)
Imports	methods, mgcv, caret, S4Vectors, stats, utils, rlang, graphics, matrixStats, tidyr
LinkingTo
Suggests	knitr, rmarkdown, testthat, BiocStyle
SystemRequirements
Enhances
URL
BugReports	https://www.github.com/hhabra/metabCombiner/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	metabCombiner_1.4.0.tar.gz
Windows Binary	metabCombiner_1.4.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	metabCombiner_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/metabCombiner
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/metabCombiner
Package Short Url	https://bioconductor.org/packages/metabCombiner/
Package Downloads Report	Download Stats