Package Recipe 'bioconductor-netomics'

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:

on bioconductor-annotationdbi >=1.64.0,<1.65.0
on bioconductor-go.db >=3.18.0,<3.19.0
on bioconductor-minet >=3.60.0,<3.61.0
on bioconductor-randomwalkrestartmh >=1.22.0,<1.23.0
on r-base >=4.3,<4.4.0a0
on r-dplyr
on r-ggplot2
on r-gprofiler2
on r-igraph
on r-magrittr
on r-purrr
on r-tibble
on r-tidyr

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-netomics

to add into an existing workspace instead, run:

pixi add bioconductor-netomics

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-netomics

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-netomics

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-netomics:<tag>

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