recipe bioconductor-curatedbreastdata

Curated breast cancer gene expression data with survival and treatment information

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/curatedBreastData.html

License:

GPL (>= 2)

Recipe:

/bioconductor-curatedbreastdata/meta.yaml

Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets.

package bioconductor-curatedbreastdata

versions:

2.30.0-0,  2.28.0-0,  2.26.0-0,  2.22.0-1,  2.22.0-0,  2.20.0-0,  2.18.0-1,  2.18.0-0,  2.16.0-0, 

2.30.0-0,  2.28.0-0,  2.26.0-0,  2.22.0-1,  2.22.0-0,  2.20.0-0,  2.18.0-1,  2.18.0-0,  2.16.0-0,  2.14.0-0,  2.12.0-1,  2.10.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocstyle:

>=2.30.0,<2.31.0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-impute:

>=1.76.0,<1.77.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-xml:

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-curatedbreastdata

and update with::

   mamba update bioconductor-curatedbreastdata

To create a new environment, run:

mamba create --name myenvname bioconductor-curatedbreastdata

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-curatedbreastdata:<tag>

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

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