:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-metnet' .. highlight: bash bioconductor-metnet =================== .. conda:recipe:: bioconductor-metnet :replaces_section_title: :noindex: Inferring metabolic networks from untargeted high\-resolution mass spectrometry data :homepage: https://bioconductor.org/packages/3.18/bioc/html/MetNet.html :license: GPL (>= 3) :recipe: /`bioconductor-metnet `_/`meta.yaml `_ 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. .. conda:package:: bioconductor-metnet |downloads_bioconductor-metnet| |docker_bioconductor-metnet| :versions: .. raw:: html
1.20.0-01.18.0-01.16.0-01.12.0-01.8.0-11.8.0-01.6.0-01.4.0-01.2.0-1 ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.12.0-0``,  ``1.8.0-1``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-1``,  ``1.0.0-0`` .. raw:: html
:depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-genie3: ``>=1.24.0,<1.25.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-bnlearn: ``>=4.3`` :depends r-corpcor: ``>=1.6.10`` :depends r-dplyr: ``>=1.0.3`` :depends r-genenet: ``>=1.2.15`` :depends r-ggplot2: ``>=3.3.3`` :depends r-parmigene: ``>=1.0.2`` :depends r-psych: ``>=2.1.6`` :depends r-rlang: ``>=0.4.10`` :depends r-stabs: ``>=0.6`` :depends r-tibble: ``>=3.0.5`` :depends r-tidyr: ``>=1.1.2`` :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install bioconductor-metnet and update with:: mamba update bioconductor-metnet To create a new environment, run:: mamba create --name myenvname bioconductor-metnet with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/bioconductor-metnet: (see `bioconductor-metnet/tags`_ for valid values for ````) .. |downloads_bioconductor-metnet| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-metnet.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-metnet :alt: (downloads) .. |docker_bioconductor-metnet| image:: https://quay.io/repository/biocontainers/bioconductor-metnet/status :target: https://quay.io/repository/biocontainers/bioconductor-metnet .. _`bioconductor-metnet/tags`: https://quay.io/repository/biocontainers/bioconductor-metnet?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-metnet/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-metnet/README.html