recipe bioconductor-netomics

Multi-Omics (time-course) network-based integration and interpretation

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-netomics/meta.yaml

netOmics is a multi-omics networks builder and explorer. It uses a combination of network inference algorithms and and knowledge-based graphs to build multi-layered networks. The package can be combined with timeOmics to incorporate time-course expression data and build sub-networks from multi-omics kinetic clusters. Finally, from the generated multi-omics networks, propagation analyses allow the identification of missing biological functions (1), multi-omics mechanisms (2) and molecules between kinetic clusters (3). This helps to resolve complex regulatory mechanisms.

package bioconductor-netomics

versions:

1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-go.db:

>=3.18.0,<3.19.0

depends bioconductor-minet:

>=3.60.0,<3.61.0

depends bioconductor-randomwalkrestartmh:

>=1.22.0,<1.23.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-gprofiler2:

depends r-igraph:

depends r-magrittr:

depends r-purrr:

depends r-tibble:

depends r-tidyr:

requirements:

additional platforms:

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-netomics

and update with::

   mamba update bioconductor-netomics

To create a new environment, run:

mamba create --name myenvname bioconductor-netomics

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-netomics:<tag>

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

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-netomics/README.html)