This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see MetNet.
Bioconductor version: 3.12
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 matrices are combined to form a adjacency matrix inferred from both quantitative and structure information.
Author: Thomas Naake [aut, cre]
Maintainer: Thomas Naake <thomasnaake at googlemail.com>
Citation (from within R,
enter citation("MetNet")
):
To install this package, start R (version "4.0") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("MetNet")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MetNet")
HTML | R Script | Workflow for high-resolution metabolomics data |
Reference Manual | ||
Text | NEWS |
biocViews | ImmunoOncology, MassSpectrometry, Metabolomics, Network, Regression, Software |
Version | 1.8.0 |
In Bioconductor since | BioC 3.8 (R-3.5) (2.5 years) |
License | GPL (>= 3) |
Depends | R (>= 3.6) |
Imports | bnlearn (>= 4.3), BiocParallel(>= 1.12.0), GENIE3(>= 1.7.0), methods (>= 3.5), mpmi (>= 0.42), parmigene (>= 1.0.2), ppcor (>= 1.1), sna (>= 2.4), stabs (>= 0.6), stats (>= 3.6) |
LinkingTo | |
Suggests | BiocGenerics(>= 0.24.0), BiocStyle(>= 2.6.1), glmnet (>= 2.0-18), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1) |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
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Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | MetNet_1.8.0.tar.gz |
Windows Binary | MetNet_1.8.0.zip |
macOS 10.13 (High Sierra) | MetNet_1.8.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/MetNet |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MetNet |
Package Short Url | https://bioconductor.org/packages/MetNet/ |
Package Downloads Report | Download Stats |
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