:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-sparrow' .. highlight: bash bioconductor-sparrow ==================== .. conda:recipe:: bioconductor-sparrow :replaces_section_title: :noindex: Take command of set enrichment analyses through a unified interface :homepage: https://bioconductor.org/packages/3.18/bioc/html/sparrow.html :license: MIT + file LICENSE :recipe: /`bioconductor-sparrow `_/`meta.yaml `_ Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package. .. conda:package:: bioconductor-sparrow |downloads_bioconductor-sparrow| |docker_bioconductor-sparrow| :versions: ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.0.1-0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biocset: ``>=1.16.0,<1.17.0`` :depends bioconductor-complexheatmap: ``>=2.18.0,<2.19.0`` :depends bioconductor-delayedmatrixstats: ``>=1.24.0,<1.25.0`` :depends bioconductor-edger: ``>=4.0.0,<4.1.0`` :depends bioconductor-gseabase: ``>=1.64.0,<1.65.0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends r-babelgene: ``>=21.4`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-checkmate: :depends r-circlize: :depends r-data.table: ``>=1.10.4`` :depends r-ggplot2: ``>=2.2.0`` :depends r-irlba: :depends r-matrix: :depends r-plotly: ``>=4.9.0`` :depends r-viridis: :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-sparrow and update with:: mamba update bioconductor-sparrow To create a new environment, run:: mamba create --name myenvname bioconductor-sparrow 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-sparrow: (see `bioconductor-sparrow/tags`_ for valid values for ````) .. |downloads_bioconductor-sparrow| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-sparrow.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-sparrow :alt: (downloads) .. |docker_bioconductor-sparrow| image:: https://quay.io/repository/biocontainers/bioconductor-sparrow/status :target: https://quay.io/repository/biocontainers/bioconductor-sparrow .. _`bioconductor-sparrow/tags`: https://quay.io/repository/biocontainers/bioconductor-sparrow?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-sparrow/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-sparrow/README.html