Package Recipe 'bioconductor-inetgrate'

recipe bioconductor-inetgrate

Integrates DNA methylation data with gene expression in a single gene network

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/iNETgrate.html
License:: GPL-3
Recipe:: /bioconductor-inetgrate/meta.yaml

The iNETgrate package provides functions to build a correlation network in which nodes are genes. DNA methylation and gene expression data are integrated to define the connections between genes. This network is used to identify modules (clusters) of genes. The biological information in each of the resulting modules is represented by an eigengene. These biological signatures can be used as features e.g., for classification of patients into risk categories. The resulting biological signatures are very robust and give a holistic view of the underlying molecular changes.

package bioconductor-inetgrate¶

Versions:

1.4.0-0, 1.0.0-0

Depends:

on bioconductor-biocstyle >=2.34.0,<2.35.0
on bioconductor-genomicranges >=1.58.0,<1.59.0
on bioconductor-homo.sapiens >=1.3.0,<1.4.0
on bioconductor-minfi >=1.52.0,<1.53.0
on bioconductor-pigengene >=1.32.0,<1.33.0
on bioconductor-summarizedexperiment >=1.36.0,<1.37.0
on r-base >=4.4,<4.5.0a0
on r-caret
on r-glmnet
on r-gplots
on r-igraph
on r-matrixstats
on r-rfast
on r-survival
on r-tidyr
on r-tidyselect
on r-wgcna

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-inetgrate

to add into an existing workspace instead, run:

pixi add bioconductor-inetgrate

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-inetgrate

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-inetgrate

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-inetgrate:<tag>

(see bioconductor-inetgrate/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-inetgrate/README.html)