metabCombiner
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see metabCombiner.
Method for Combining LC-MS Metabolomics Feature Measurements
Bioconductor version: 3.16
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("metabCombiner")):
Installation
To install this package, start R (version "4.2") 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 | ||
| NEWS | Text |
Details
| biocViews | MassSpectrometry, Metabolomics, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.0), dplyr (>= 1.0) |
| Imports | 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_1.8.0.tar.gz |
| Windows Binary | metabCombiner_1.8.0.zip |
| macOS Binary (x86_64) | metabCombiner_1.8.0.tgz |
| macOS Binary (arm64) | metabCombiner_1.8.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |