recipe bioconductor-inetgrate

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

Homepage:

https://bioconductor.org/packages/3.18/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:

1.0.0-0

depends bioconductor-biocstyle:

>=2.30.0,<2.31.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-homo.sapiens:

>=1.3.0,<1.4.0

depends bioconductor-minfi:

>=1.48.0,<1.49.0

depends bioconductor-pigengene:

>=1.28.0,<1.29.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-caret:

depends r-glmnet:

depends r-gplots:

depends r-igraph:

depends r-matrixstats:

depends r-rfast:

depends r-survival:

depends r-tidyr:

depends r-tidyselect:

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-inetgrate

and update with::

   mamba update bioconductor-inetgrate

To create a new environment, run:

mamba create --name myenvname bioconductor-inetgrate

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-inetgrate:<tag>

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

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