MetNet
This is the development version of MetNet; for the stable release version, see MetNet.
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
Bioconductor version: Development (3.24)
MetNet contains functionality to infer metabolic network topologies from quantitative data and high-resolution mass/charge information. Using statistical models (including correlation, mutual information, regression and Bayes statistics) and quantitative data (intensity values of features) adjacency matrices are inferred that can be combined to a consensus matrix. Mass differences calculated between mass/charge values of features will be matched against a data frame of supplied mass/charge differences referring to transformations of enzymatic activities. In a third step, the two levels of information are combined to form a adjacency matrix inferred from both quantitative and structure information.
Author: Thomas Naake [aut, cre], Liesa Salzer [ctb], Elva Maria Novoa-del-Toro [ctb]
Maintainer: Thomas Naake <thomasnaake at googlemail.com>
citation("MetNet")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("MetNet")
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("MetNet")| Workflow for high-resolution metabolomics data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Metabolomics, Network, Regression, Software |
| Version | 1.31.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | GPL (>= 3) |
| Depends | R (>= 4.1), S4Vectors(>= 0.28.1), SummarizedExperiment(>= 1.20.0) |
| Imports | bnlearn (>= 4.3), BiocParallel(>= 1.12.0), corpcor (>= 1.6.10), dplyr (>= 1.0.3), ggplot2 (>= 3.3.3), GeneNet (>= 1.2.15), GENIE3(>= 1.7.0), methods (>= 4.1), parmigene (>= 1.0.2), psych (>= 2.1.6), rlang (>= 0.4.10), stabs (>= 0.6), stats (>= 4.1), tibble (>= 3.0.5), tidyr (>= 1.1.2) |
| System Requirements | |
| URL |
See More
| Suggests | BiocGenerics(>= 0.24.0), BiocStyle(>= 2.6.1), glmnet (>= 4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1), Spectra(>= 1.4.1), MsCoreUtils(>= 1.6.0) |
| 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 | MetNet_1.31.0.tar.gz |
| Windows Binary (x86_64) | MetNet_1.31.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | MetNet_1.31.0.tgz |
| macOS Binary (sonoma-arm64) | MetNet_1.31.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MetNet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MetNet |
| Bioc Package Browser | https://code.bioconductor.org/browse/MetNet/ |
| Package Short Url | https://bioconductor.org/packages/MetNet/ |
| Package Downloads Report | Download Stats |