recipe bioconductor-genegeneinter

Tools for Testing Gene-Gene Interaction at the Gene Level

Homepage:

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

License:

GPL-3.0.-or-later

Recipe:

/bioconductor-genegeneinter/meta.yaml

Links:

biotools: genegeneinter

The aim of this package is to propose several methods for testing gene-gene interaction in case-control association studies. Such a test can be done by aggregating SNP-SNP interaction tests performed at the SNP level (SSI) or by using gene-gene multidimensionnal methods (GGI) methods. The package also proposes tools for a graphic display of the results. <doi:10.18637/jss.v095.i12>.

package bioconductor-genegeneinter

versions:

1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.20.0-2,  1.20.0-1,  1.20.0-0,  1.18.0-0, 

1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.20.0-2,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.0-0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.1,<1.55.0a0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0a0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0a0

depends bioconductor-snpstats:

>=1.52.0,<1.53.0

depends bioconductor-snpstats:

>=1.52.0,<1.53.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-factominer:

depends r-igraph:

depends r-kernlab:

depends r-mvtnorm:

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-genegeneinter

and update with::

   mamba update bioconductor-genegeneinter

To create a new environment, run:

mamba create --name myenvname bioconductor-genegeneinter

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-genegeneinter:<tag>

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

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