Registration and Call for Abstracts Open for Bioc2024

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 (3.19)

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 "4.4") and enter:


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

Details

biocViews MassSpectrometry, Metabolomics, Software
Version 1.13.0
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
See More
Suggests knitr, rmarkdown, testthat, BiocStyle
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 metabCombiner_1.13.0.tar.gz
Windows Binary metabCombiner_1.13.0.zip
macOS Binary (x86_64) metabCombiner_1.13.0.tgz
macOS Binary (arm64) metabCombiner_1.13.0.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