recipe bioconductor-degraph

Two-sample tests on a graph

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-degraph/meta.yaml

Links:

biotools: degraph, doi: 10.1214/11-AOAS528

DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of the network to yield more powerful detection procedures. DEGraph provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results.

package bioconductor-degraph

versions:

1.54.0-0,  1.52.0-0,  1.50.0-0,  1.46.0-0,  1.44.0-0,  1.42.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-0, 

1.54.0-0,  1.52.0-0,  1.50.0-0,  1.46.0-0,  1.44.0-0,  1.42.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-0

depends bioconductor-graph:

>=1.80.0,<1.81.0

depends bioconductor-kegggraph:

>=1.62.0,<1.63.0

depends bioconductor-ncigraph:

>=1.50.0,<1.51.0

depends bioconductor-rbgl:

>=1.78.0,<1.79.0

depends bioconductor-rgraphviz:

>=2.46.0,<2.47.0

depends r-base:

>=4.3,<4.4.0a0

depends r-lattice:

depends r-mvtnorm:

depends r-r.methodss3:

depends r-r.utils:

depends r-rrcov:

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-degraph

and update with::

   mamba update bioconductor-degraph

To create a new environment, run:

mamba create --name myenvname bioconductor-degraph

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-degraph:<tag>

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

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