metabCombiner
This is the released version of metabCombiner; for the devel version, see metabCombiner.
Method for Combining LC-MS Metabolomics Feature Measurements
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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_1.22.0.tar.gz |
| Windows Binary (x86_64) | metabCombiner_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | metabCombiner_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | metabCombiner_1.22.0.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 |