recipe bioconductor-cancersubtypes

Cancer subtypes identification, validation and visualization based on multiple genomic data sets

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/CancerSubtypes.html

License:

GPL (>= 2)

Recipe:

/bioconductor-cancersubtypes/meta.yaml

Links:

biotools: cancersubtypes, doi: 10.1038/nmeth.3252

CancerSubtypes integrates the current common computational biology methods for cancer subtypes identification and provides a standardized framework for cancer subtype analysis based multi-omics data, such as gene expression, miRNA expression, DNA methylation and others.

package bioconductor-cancersubtypes

(downloads) docker_bioconductor-cancersubtypes

versions:
1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1, 

1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0

depends bioconductor-consensusclusterplus:

>=1.64.0,<1.65.0

depends bioconductor-impute:

>=1.74.0,<1.75.0

depends bioconductor-limma:

>=3.56.0,<3.57.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cluster:

depends r-nmf:

depends r-sigclust:

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-cancersubtypes

and update with::

   mamba update bioconductor-cancersubtypes

To create a new environment, run:

mamba create --name myenvname bioconductor-cancersubtypes

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-cancersubtypes:<tag>

(see `bioconductor-cancersubtypes/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-cancersubtypes/README.html)