:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-assign' .. highlight: bash bioconductor-assign =================== .. conda:recipe:: bioconductor-assign :replaces_section_title: :noindex: Adaptive Signature Selection and InteGratioN \(ASSIGN\) :homepage: https://bioconductor.org/packages/3.18/bioc/html/ASSIGN.html :license: MIT + file LICENSE :recipe: /`bioconductor-assign `_/`meta.yaml `_ ASSIGN is a computational tool to evaluate the pathway deregulation\/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge\-based literature or from perturbation experiments to the cell\-\/tissue\-specific pathway signatures. The deregulation\/activation level of each context\-specific pathway is quantified to a score\, which represents the extent to which a patient sample encompasses the pathway deregulation\/activation signature. .. conda:package:: bioconductor-assign |downloads_bioconductor-assign| |docker_bioconductor-assign| :versions: .. raw:: html
1.38.0-01.36.0-01.34.0-01.30.0-01.28.0-01.26.0-11.26.0-01.24.0-01.22.0-0 ``1.38.0-0``,  ``1.36.0-0``,  ``1.34.0-0``,  ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-1``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.1-1``,  ``1.18.0-0`` .. raw:: html
:depends bioconductor-sva: ``>=3.50.0,<3.51.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-ggplot2: :depends r-gplots: :depends r-msm: :depends r-rlab: :depends r-yaml: :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-assign and update with:: mamba update bioconductor-assign To create a new environment, run:: mamba create --name myenvname bioconductor-assign 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-assign: (see `bioconductor-assign/tags`_ for valid values for ````) .. |downloads_bioconductor-assign| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-assign.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-assign :alt: (downloads) .. |docker_bioconductor-assign| image:: https://quay.io/repository/biocontainers/bioconductor-assign/status :target: https://quay.io/repository/biocontainers/bioconductor-assign .. _`bioconductor-assign/tags`: https://quay.io/repository/biocontainers/bioconductor-assign?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-assign/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-assign/README.html