:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'r-dnet' .. highlight: bash r-dnet ====== .. conda:recipe:: r-dnet :replaces_section_title: :noindex: The focus of the dnet by Fang and Gough \(2014\) \ is to make sense of omics data \(such as gene expression and mutations\) from different angles including\: integration with molecular networks\, enrichments using ontologies\, and relevance to gene evolutionary ages. Integration is achieved to identify a gene subnetwork from the whole gene network whose nodes\/genes are labelled with informative data \(such as the significant levels of differential expression or survival risks\). To help make sense of identified gene networks\, enrichment analysis is also supported using a wide variety of pre\-compiled ontologies and phylostratific gene age information in major organisms including\: human\, mouse\, rat\, chicken\, C.elegans\, fruit fly\, zebrafish and arabidopsis. Add\-on functionalities are supports for calculating semantic similarity between ontology terms \(and between genes\) and for calculating network affinity based on random walk\; both can be done via high\-performance parallel computing. :homepage: http://dnet.r-forge.r-project.org, https://github.com/hfang-bristol/dnet :license: GPL2 / GPL-2 :recipe: /`r-dnet `_/`meta.yaml `_ .. conda:package:: r-dnet |downloads_r-dnet| |docker_r-dnet| :versions: .. raw:: html
1.1.7-51.1.7-41.1.7-31.1.7-21.1.7-11.1.7-01.1.6-01.1.5-01.1.4-1 ``1.1.7-5``,  ``1.1.7-4``,  ``1.1.7-3``,  ``1.1.7-2``,  ``1.1.7-1``,  ``1.1.7-0``,  ``1.1.6-0``,  ``1.1.5-0``,  ``1.1.4-1``,  ``1.1.4-0`` .. raw:: html
:depends bioconductor-graph: :depends bioconductor-rgraphviz: :depends bioconductor-suprahex: :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-igraph: :depends r-matrix: :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 r-dnet and update with:: mamba update r-dnet To create a new environment, run:: mamba create --name myenvname r-dnet 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/r-dnet: (see `r-dnet/tags`_ for valid values for ````) .. |downloads_r-dnet| image:: https://img.shields.io/conda/dn/bioconda/r-dnet.svg?style=flat :target: https://anaconda.org/bioconda/r-dnet :alt: (downloads) .. |docker_r-dnet| image:: https://quay.io/repository/biocontainers/r-dnet/status :target: https://quay.io/repository/biocontainers/r-dnet .. _`r-dnet/tags`: https://quay.io/repository/biocontainers/r-dnet?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/r-dnet/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/r-dnet/README.html