:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-multigsea' .. highlight: bash bioconductor-multigsea ====================== .. conda:recipe:: bioconductor-multigsea :replaces_section_title: :noindex: Combining GSEA\-based pathway enrichment with multi omics data integration :homepage: https://bioconductor.org/packages/3.18/bioc/html/multiGSEA.html :license: GPL-3 :recipe: /`bioconductor-multigsea `_/`meta.yaml `_ Extracted features from pathways derived from 8 different databases \(KEGG\, Reactome\, Biocarta\, etc.\) can be used on transcriptomic\, proteomic\, and\/or metabolomic level to calculate a combined GSEA\-based enrichment score. .. conda:package:: bioconductor-multigsea |downloads_bioconductor-multigsea| |docker_bioconductor-multigsea| :versions: ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.1-1``,  ``1.0.1-0``,  ``1.0.0-1`` :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0`` :depends bioconductor-fgsea: ``>=1.28.0,<1.29.0`` :depends bioconductor-graphite: ``>=1.48.0,<1.49.0`` :depends bioconductor-metaboliteidmapping: ``>=1.0.0,<1.1.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-dplyr: :depends r-magrittr: :depends r-metap: :depends r-rappdirs: :depends r-rlang: :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-multigsea and update with:: mamba update bioconductor-multigsea To create a new environment, run:: mamba create --name myenvname bioconductor-multigsea 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-multigsea: (see `bioconductor-multigsea/tags`_ for valid values for ````) .. |downloads_bioconductor-multigsea| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-multigsea.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-multigsea :alt: (downloads) .. |docker_bioconductor-multigsea| image:: https://quay.io/repository/biocontainers/bioconductor-multigsea/status :target: https://quay.io/repository/biocontainers/bioconductor-multigsea .. _`bioconductor-multigsea/tags`: https://quay.io/repository/biocontainers/bioconductor-multigsea?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-multigsea/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-multigsea/README.html