MetNet

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see MetNet.

Inferring metabolic networks from untargeted high-resolution mass spectrometry data


Bioconductor version: 3.16

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]

Maintainer: Thomas Naake <thomasnaake at googlemail.com>

Citation (from within R, enter citation("MetNet")):

Installation

To install this package, start R (version "4.2") and enter:


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

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 PDF
NEWS Text

Details

biocViews ImmunoOncology, MassSpectrometry, Metabolomics, Network, Regression, Software
Version 1.16.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL (>= 3)
Depends R (>= 4.0), 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 (>= 3.5), parmigene (>= 1.0.2), psych (>= 2.1.6), rlang (>= 0.4.10), stabs (>= 0.6), stats (>= 3.6), tibble (>= 3.0.5), tidyr (>= 1.1.2)
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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)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MetNet_1.16.0.tar.gz
Windows Binary MetNet_1.16.0.zip
macOS Binary (x86_64) MetNet_1.16.0.tgz
macOS Binary (arm64) MetNet_1.16.0.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
Old Source Packages for BioC 3.16 Source Archive