recipe bioconductor-genefu

Computation of Gene Expression-Based Signatures in Breast Cancer

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/genefu.html

License:

Artistic-2.0

Recipe:

/bioconductor-genefu/meta.yaml

Links:

biotools: genefu, doi: 10.1093/bioinformatics/btv693

This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.

package bioconductor-genefu

versions:

2.34.0-0,  2.32.0-0,  2.30.0-0,  2.26.0-0,  2.24.2-0,  2.22.1-0,  2.22.0-0,  2.20.0-0,  2.18.0-0, 

2.34.0-0,  2.32.0-0,  2.30.0-0,  2.26.0-0,  2.24.2-0,  2.22.1-0,  2.22.0-0,  2.20.0-0,  2.18.0-0,  2.16.0-1,  2.14.0-0,  2.12.0-0,  2.10.0-0

depends bioconductor-aims:

>=1.34.0,<1.35.0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-impute:

>=1.76.0,<1.77.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-survcomp:

>=1.52.0,<1.53.0

depends r-amap:

depends r-base:

>=4.3,<4.4.0a0

depends r-ic10:

depends r-mclust:

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-genefu

and update with::

   mamba update bioconductor-genefu

To create a new environment, run:

mamba create --name myenvname bioconductor-genefu

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-genefu:<tag>

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

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