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(https://travis-ci.com/abodein/netOmics)

[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)]

(https://www.gnu.org/licenses/gpl-3.0)

# netOmics

With netOmics, we go beyond integration by introducing an interpretation tool.

netOmics is a package for the creation and exploration of multi-omics networks.

Depending on the provided dataset, it allows to create inference networks from 

expression data but also interaction networks from knowledge databases.

After merging the sub-networks to obtain a global multi-omics network, 

we propose network exploration methods using propoagation techniques to perform 

functional prediction or identification of molecular mechanisms.

Furthermore, the package has been developed for longitudinal multi-omics data 

and can be used in conjunction with our previously published package timeOmics.

for more examples, please visite 

https://github.com/abodein/netOmics-case-studies

## Installation

### Latest `BioConductor` Release

To install this package, start R (version "4.1") and enter: 

```r

if (!requireNamespace("BiocManager", quietly = TRUE))

    install.packages("BiocManager")

BiocManager::install("netOmics")

```

### Latest `GitHub` Version

Install the devtools package in R, then load it and install the latest stable 

version of `netOmics` from `GitHub`

```r

## install devtools if not installed

if (!requireNamespace("devtools", quietly = TRUE))

    install.packages("devtools")

## install netOmics

devtools::install_github("abodein/netOmics")

```

## Citing

*"Bodein, A., Scott-Boyer, M. P., Perin, O., Le Cao, K. A., & Droit, A. (2020). 

Interpretation of network-based integration from multi-omics longitudinal data. 

bioRxiv."*

## Maintainer

Antoine Bodein (<antoine.bodein.1@ulaval.ca>)

## Bugs/Feature requests

If you have any bugs or feature requests, 

[let us know](https://github.com/abodein/netOmics/issues). 

Thanks!