recipe bioconductor-stroma4

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).

package bioconductor-stroma4

(downloads) docker_bioconductor-stroma4

versions:
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, 

1.24.0-0,  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

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:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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:<tag>

(see `bioconductor-stroma4/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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