:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-famat' .. highlight: bash bioconductor-famat ================== .. conda:recipe:: bioconductor-famat :replaces_section_title: :noindex: Functional analysis of metabolic and transcriptomic data :homepage: https://bioconductor.org/packages/3.14/bioc/html/famat.html :license: GPL-3 :recipe: /`bioconductor-famat `_/`meta.yaml `_ Famat is made to collect data about lists of genes and metabolites provided by user\, and to visualize it through a Shiny app. Information collected is\: \- Pathways containing some of the user\'s genes and metabolites \(obtained using a pathway enrichment analysis\). \- Direct interactions between user\'s elements inside pathways. \- Information about elements \(their identifiers and descriptions\). \- Go terms enrichment analysis performed on user\'s genes. The Shiny app is composed of\: \- information about genes\, metabolites\, and direct interactions between them inside pathways. \- an heatmap showing which elements from the list are in pathways \(pathways are structured in hierarchies\). \- hierarchies of enriched go terms using Molecular Function and Biological Process. .. conda:package:: bioconductor-famat |downloads_bioconductor-famat| |docker_bioconductor-famat| :versions: ``1.4.0-0``,  ``1.1.1-0``,  ``1.0.0-1``,  ``1.0.0-0`` :depends bioconductor-clusterprofiler: ``>=4.2.0,<4.3.0`` :depends bioconductor-go.db: ``>=3.14.0,<3.15.0`` :depends bioconductor-keggrest: ``>=1.34.0,<1.35.0`` :depends bioconductor-org.hs.eg.db: ``>=3.14.0,<3.15.0`` :depends bioconductor-reactome.db: ``>=1.77.0,<1.78.0`` :depends bioconductor-rwikipathways: ``>=1.14.0,<1.15.0`` :depends r-base: ``>=4.1,<4.2.0a0`` :depends r-dplyr: :depends r-dt: :depends r-gprofiler2: :depends r-magrittr: :depends r-mpinet: :depends r-ontologyindex: :depends r-plotly: :depends r-shiny: :depends r-shinybs: :depends r-shinydashboard: :depends r-stringr: :depends r-tidyr: :requirements: .. rubric:: Installation With an activated Bioconda channel (see :ref:`set-up-channels`), install with:: conda install bioconductor-famat and update with:: conda update bioconductor-famat or use the docker container:: docker pull quay.io/biocontainers/bioconductor-famat: (see `bioconductor-famat/tags`_ for valid values for ````) .. |downloads_bioconductor-famat| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-famat.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-famat :alt: (downloads) .. |docker_bioconductor-famat| image:: https://quay.io/repository/biocontainers/bioconductor-famat/status :target: https://quay.io/repository/biocontainers/bioconductor-famat .. _`bioconductor-famat/tags`: https://quay.io/repository/biocontainers/bioconductor-famat?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-famat/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-famat/README.html