:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-gmicr' .. highlight: bash bioconductor-gmicr ================== .. conda:recipe:: bioconductor-gmicr :replaces_section_title: :noindex: Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene\-Module Immune\-Cell network \(GMIC\) :homepage: https://bioconductor.org/packages/3.18/bioc/html/GmicR.html :license: GPL-2 + file LICENSE :recipe: /`bioconductor-gmicr `_/`meta.yaml `_ This package uses bayesian network learning to detect relationships between Gene Modules detected by WGCNA and immune cell signatures defined by xCell. It is a hypothesis generating tool. .. conda:package:: bioconductor-gmicr |downloads_bioconductor-gmicr| |docker_bioconductor-gmicr| :versions: ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-0`` :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0`` :depends bioconductor-category: ``>=2.68.0,<2.69.0`` :depends bioconductor-gostats: ``>=2.68.0,<2.69.0`` :depends bioconductor-gseabase: ``>=1.64.0,<1.65.0`` :depends bioconductor-org.hs.eg.db: ``>=3.18.0,<3.19.0`` :depends bioconductor-org.mm.eg.db: ``>=3.18.0,<3.19.0`` :depends r-ape: :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-bnlearn: :depends r-data.table: :depends r-doparallel: :depends r-dt: :depends r-foreach: :depends r-grain: :depends r-grbase: :depends r-reshape2: :depends r-shiny: :depends r-wgcna: :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-gmicr and update with:: mamba update bioconductor-gmicr To create a new environment, run:: mamba create --name myenvname bioconductor-gmicr 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-gmicr: (see `bioconductor-gmicr/tags`_ for valid values for ````) .. |downloads_bioconductor-gmicr| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-gmicr.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-gmicr :alt: (downloads) .. |docker_bioconductor-gmicr| image:: https://quay.io/repository/biocontainers/bioconductor-gmicr/status :target: https://quay.io/repository/biocontainers/bioconductor-gmicr .. _`bioconductor-gmicr/tags`: https://quay.io/repository/biocontainers/bioconductor-gmicr?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-gmicr/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-gmicr/README.html