:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-pathifier' .. highlight: bash bioconductor-pathifier ====================== .. conda:recipe:: bioconductor-pathifier :replaces_section_title: :noindex: Quantify deregulation of pathways in cancer :homepage: https://bioconductor.org/packages/3.18/bioc/html/pathifier.html :license: Artistic-1.0 :recipe: /`bioconductor-pathifier `_/`meta.yaml `_ :links: biotools: :biotools:`pathifier`, doi: :doi:`10.1073/pnas.1219651110` Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined\, in a context\-specific manner\, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene\-level information into pathway\-level information\, generating a compact and biologically relevant representation of each sample. .. conda:package:: bioconductor-pathifier |downloads_bioconductor-pathifier| |docker_bioconductor-pathifier| :versions: .. raw:: html
1.40.0-01.38.0-01.36.0-01.32.0-01.30.0-01.28.0-11.28.0-01.26.0-01.24.0-0 ``1.40.0-0``,  ``1.38.0-0``,  ``1.36.0-0``,  ``1.32.0-0``,  ``1.30.0-0``,  ``1.28.0-1``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.20.0-1``,  ``1.20.0-0``,  ``1.16.0-0`` .. raw:: html
:depends r-base: ``>=4.3,<4.4.0a0`` :depends r-princurve: ``>=2.0.4`` :depends r-r.oo: :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-pathifier and update with:: mamba update bioconductor-pathifier To create a new environment, run:: mamba create --name myenvname bioconductor-pathifier 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-pathifier: (see `bioconductor-pathifier/tags`_ for valid values for ````) .. |downloads_bioconductor-pathifier| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-pathifier.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-pathifier :alt: (downloads) .. |docker_bioconductor-pathifier| image:: https://quay.io/repository/biocontainers/bioconductor-pathifier/status :target: https://quay.io/repository/biocontainers/bioconductor-pathifier .. _`bioconductor-pathifier/tags`: https://quay.io/repository/biocontainers/bioconductor-pathifier?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-pathifier/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-pathifier/README.html