:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-phenotest' .. highlight: bash bioconductor-phenotest ====================== .. conda:recipe:: bioconductor-phenotest :replaces_section_title: :noindex: Tools to test association between gene expression and phenotype in a way that is efficient\, structured\, fast and scalable. We also provide tools to do GSEA \(Gene set enrichment analysis\) and copy number variation. :homepage: https://bioconductor.org/packages/3.18/bioc/html/phenoTest.html :license: GPL (>=2) :recipe: /`bioconductor-phenotest `_/`meta.yaml `_ Tools to test correlation between gene expression and phenotype in a way that is efficient\, structured\, fast and scalable. GSEA is also provided. .. conda:package:: bioconductor-phenotest |downloads_bioconductor-phenotest| |docker_bioconductor-phenotest| :versions: .. raw:: html
1.50.0-01.48.0-01.46.0-01.42.0-01.40.0-01.38.0-11.38.0-01.36.0-01.34.0-0 ``1.50.0-0``,  ``1.48.0-0``,  ``1.46.0-0``,  ``1.42.0-0``,  ``1.40.0-0``,  ``1.38.0-1``,  ``1.38.0-0``,  ``1.36.0-0``,  ``1.34.0-0``,  ``1.32.0-1``,  ``1.30.0-0`` .. raw:: html
:depends bioconductor-annotate: ``>=1.80.0,<1.81.0`` :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0`` :depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-biomart: ``>=2.58.0,<2.59.0`` :depends bioconductor-category: ``>=2.68.0,<2.69.0`` :depends bioconductor-genefilter: ``>=1.84.0,<1.85.0`` :depends bioconductor-gseabase: ``>=1.64.0,<1.65.0`` :depends bioconductor-heatplus: ``>=3.10.0,<3.11.0`` :depends bioconductor-hgu133a.db: ``>=3.13.0,<3.14.0`` :depends bioconductor-hopach: ``>=2.62.0,<2.63.0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-bma: :depends r-ellipse: :depends r-ggplot2: :depends r-gplots: :depends r-hmisc: :depends r-mgcv: :depends r-survival: :depends r-xtable: :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-phenotest and update with:: mamba update bioconductor-phenotest To create a new environment, run:: mamba create --name myenvname bioconductor-phenotest 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-phenotest: (see `bioconductor-phenotest/tags`_ for valid values for ````) .. |downloads_bioconductor-phenotest| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-phenotest.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-phenotest :alt: (downloads) .. |docker_bioconductor-phenotest| image:: https://quay.io/repository/biocontainers/bioconductor-phenotest/status :target: https://quay.io/repository/biocontainers/bioconductor-phenotest .. _`bioconductor-phenotest/tags`: https://quay.io/repository/biocontainers/bioconductor-phenotest?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-phenotest/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-phenotest/README.html