Package Recipe 'bioconductor-degraph'

recipe bioconductor-degraph

Two-sample tests on a graph

Homepage:: https://bioconductor.org/packages/3.20/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:

1.62.0-0, 1.58.0-0, 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,

1.62.0-0, 1.58.0-0, 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:

on bioconductor-graph >=1.88.0,<1.89.0
on bioconductor-kegggraph >=1.70.0,<1.71.0
on bioconductor-ncigraph >=1.58.0,<1.59.0
on bioconductor-rbgl >=1.86.0,<1.87.0
on bioconductor-rgraphviz >=2.54.0,<2.55.0
on r-base >=4.5,<4.6.0a0
on r-lattice
on r-mvtnorm
on r-r.methodss3
on r-r.utils
on r-rrcov

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-degraph

to add into an existing workspace instead, run:

pixi add bioconductor-degraph

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-degraph

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-degraph

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-degraph:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-degraph/README.html)