recipe bioconductor-csdr

Differential gene co-expression

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-csdr/meta.yaml

This package contains functionality to run differential gene co-expression across two different conditions. The algorithm is inspired by Voigt et al. 2017 and finds Conserved, Specific and Differentiated genes (hence the name CSD). This package include efficient and variance calculation by bootstrapping and Welford's algorithm.

package bioconductor-csdr

versions:

1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.0.0-2,  1.0.0-1,  1.0.0-0

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-glue:

depends r-matrixstats:

depends r-rcpp:

depends r-rhpcblasctl:

depends r-wgcna:

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-csdr

and update with::

   mamba update bioconductor-csdr

To create a new environment, run:

mamba create --name myenvname bioconductor-csdr

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-csdr:<tag>

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

Download stats

Link to this page

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