metabCombiner

DOI: 10.18129/B9.bioc.metabCombiner    

This is the development version of metabCombiner; for the stable release version, see metabCombiner.

Method for Combining LC-MS Metabolomics Feature Measurements

Bioconductor version: Development (3.13)

This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Two peak-picked and 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 "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License GPL-3
Depends R (>= 4.0), dplyr (>= 1.0)
Imports methods, mgcv, caret, S4Vectors, stats, utils, rlang, graphics, matrixStats
LinkingTo
Suggests knitr, rmarkdown, testthat
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_1.1.0.tar.gz
Windows Binary metabCombiner_1.1.0.zip
macOS 10.13 (High Sierra) metabCombiner_1.1.0.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/
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