:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-sspaths' .. highlight: bash bioconductor-sspaths ==================== .. conda:recipe:: bioconductor-sspaths :replaces_section_title: :noindex: ssPATHS\: Single Sample PATHway Score :homepage: https://bioconductor.org/packages/3.18/bioc/html/ssPATHS.html :license: MIT + file LICENSE :recipe: /`bioconductor-sspaths `_/`meta.yaml `_ This package generates pathway scores from expression data for single samples after training on a reference cohort. The score is generated by taking the expression of a gene set \(pathway\) from a reference cohort and performing linear discriminant analysis to distinguish samples in the cohort that have the pathway augmented and not. The separating hyperplane is then used to score new samples. .. conda:package:: bioconductor-sspaths |downloads_bioconductor-sspaths| |docker_bioconductor-sspaths| :versions: ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-dml: :depends r-mess: :depends r-rocr: :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-sspaths and update with:: mamba update bioconductor-sspaths To create a new environment, run:: mamba create --name myenvname bioconductor-sspaths 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-sspaths: (see `bioconductor-sspaths/tags`_ for valid values for ````) .. |downloads_bioconductor-sspaths| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-sspaths.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-sspaths :alt: (downloads) .. |docker_bioconductor-sspaths| image:: https://quay.io/repository/biocontainers/bioconductor-sspaths/status :target: https://quay.io/repository/biocontainers/bioconductor-sspaths .. _`bioconductor-sspaths/tags`: https://quay.io/repository/biocontainers/bioconductor-sspaths?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-sspaths/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-sspaths/README.html