:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-stroma4' .. highlight: bash bioconductor-stroma4 ==================== .. conda:recipe:: bioconductor-stroma4 :replaces_section_title: :noindex: Assign Properties to TNBC Patients :homepage: https://bioconductor.org/packages/3.17/bioc/html/STROMA4.html :license: GPL-3 :recipe: /`bioconductor-stroma4 `_/`meta.yaml `_ This package estimates four stromal properties identified in TNBC patients in each patient of a gene expression datasets. These stromal property assignments can be combined to subtype patients. These four stromal properties were identified in Triple negative breast cancer \(TNBC\) patients and represent the presence of different cells in the stroma\: T\-cells \(T\)\, B\-cells \(B\)\, stromal infiltrating epithelial cells \(E\)\, and desmoplasia \(D\). Additionally this package can also be used to estimate generative properties for the Lehmann subtypes\, an alternative TNBC subtyping scheme \(PMID\: 21633166\). .. conda:package:: bioconductor-stroma4 |downloads_bioconductor-stroma4| |docker_bioconductor-stroma4| :versions: .. raw:: html
1.24.0-01.22.0-01.18.0-01.16.0-01.14.0-11.14.0-01.12.0-01.10.0-01.8.0-1 ``1.24.0-0``,  ``1.22.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-1``,  ``1.6.1-0``,  ``1.6.0-0`` .. raw:: html
:depends bioconductor-biobase: ``>=2.60.0,<2.61.0`` :depends bioconductor-biocparallel: ``>=1.34.0,<1.35.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-cluster: :depends r-matrixstats: :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-stroma4 and update with:: mamba update bioconductor-stroma4 To create a new environment, run:: mamba create --name myenvname bioconductor-stroma4 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-stroma4: (see `bioconductor-stroma4/tags`_ for valid values for ````) .. |downloads_bioconductor-stroma4| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-stroma4.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-stroma4 :alt: (downloads) .. |docker_bioconductor-stroma4| image:: https://quay.io/repository/biocontainers/bioconductor-stroma4/status :target: https://quay.io/repository/biocontainers/bioconductor-stroma4 .. _`bioconductor-stroma4/tags`: https://quay.io/repository/biocontainers/bioconductor-stroma4?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-stroma4/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-stroma4/README.html