recipe bioconductor-edge

Extraction of Differential Gene Expression

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-edge/meta.yaml

The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and generalized likelihood ratio tests (equivalent to F-tests and t-tests) are implemented for general study designs. Special functions are available to facilitate the analysis of common study designs, including time course experiments. Other packages such as snm, sva, and qvalue are integrated in edge to provide a wide range of tools for gene expression analysis.

package bioconductor-edge

versions:

2.34.0-0,  2.32.0-0,  2.30.0-1,  2.30.0-0,  2.26.0-2,  2.26.0-1,  2.26.0-0,  2.24.0-0,  2.22.0-1, 

2.34.0-0,  2.32.0-0,  2.30.0-1,  2.30.0-0,  2.26.0-2,  2.26.0-1,  2.26.0-0,  2.24.0-0,  2.22.0-1,  2.22.0-0,  2.20.0-0,  2.18.0-0,  2.16.0-1,  2.14.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0a0

depends bioconductor-qvalue:

>=2.34.0,<2.35.0

depends bioconductor-qvalue:

>=2.34.0,<2.35.0a0

depends bioconductor-snm:

>=1.50.0,<1.51.0

depends bioconductor-snm:

>=1.50.0,<1.51.0a0

depends bioconductor-sva:

>=3.50.0,<3.51.0

depends bioconductor-sva:

>=3.50.0,<3.51.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-mass:

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-edge

and update with::

   mamba update bioconductor-edge

To create a new environment, run:

mamba create --name myenvname bioconductor-edge

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-edge:<tag>

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

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