:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'r-mgsz' .. highlight: bash r-mgsz ====== .. conda:recipe:: r-mgsz :replaces_section_title: :noindex: Performs gene set analysis based on GSZ scoring function and asymptotic p\-value. It is different from GSZ in that it implements asymptotic p\-values instead of empirical p\-values. Asymptotic p\-values are calculated by fitting suitable distribution model to the null distribution. Unlike empirical p\-values\, resolution of asymptotic p\-values are independent of the number of permutations and hence requires considerably fewer permutations. In addition\, this package allows gene set analysis with seven other popular gene set analysis methods. :homepage: https://CRAN.R-project.org/package=mGSZ :license: GPL3 / GPL (>= 2) :recipe: /`r-mgsz `_/`meta.yaml `_ .. conda:package:: r-mgsz |downloads_r-mgsz| |docker_r-mgsz| :versions: ``1.0-5``,  ``1.0-4``,  ``1.0-3``,  ``1.0-2``,  ``1.0-1``,  ``1.0-0`` :depends bioconductor-biobase: :depends bioconductor-limma: :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-gsa: :depends r-ismev: :depends r-mass: :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-mgsz and update with:: mamba update r-mgsz To create a new environment, run:: mamba create --name myenvname r-mgsz 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-mgsz: (see `r-mgsz/tags`_ for valid values for ````) .. |downloads_r-mgsz| image:: https://img.shields.io/conda/dn/bioconda/r-mgsz.svg?style=flat :target: https://anaconda.org/bioconda/r-mgsz :alt: (downloads) .. |docker_r-mgsz| image:: https://quay.io/repository/biocontainers/r-mgsz/status :target: https://quay.io/repository/biocontainers/r-mgsz .. _`r-mgsz/tags`: https://quay.io/repository/biocontainers/r-mgsz?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-mgsz/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-mgsz/README.html