recipe bioconductor-tnbc.cms

TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/TNBC.CMS.html

License:

GPL-3

Recipe:

/bioconductor-tnbc.cms/meta.yaml

This package implements a machine learning-based classifier for the assignment of consensus molecular subtypes to TNBC samples. It also provides functions to summarize genomic and clinical characteristics.

package bioconductor-tnbc.cms

(downloads) docker_bioconductor-tnbc.cms

versions:
1.18.0-0,  1.16.0-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0, 

1.18.0-0,  1.16.0-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

depends bioconductor-gsva:

>=1.50.0,<1.51.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-e1071:

depends r-forestplot:

depends r-ggally:

depends r-ggplot2:

depends r-ggpubr:

depends r-pheatmap:

depends r-pracma:

depends r-quadprog:

depends r-r.utils:

depends r-rcolorbrewer:

depends r-survival:

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-tnbc.cms

and update with::

   mamba update bioconductor-tnbc.cms

To create a new environment, run:

mamba create --name myenvname bioconductor-tnbc.cms

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-tnbc.cms:<tag>

(see `bioconductor-tnbc.cms/tags`_ for valid values for ``<tag>``)

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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-tnbc.cms/README.html)