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:

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

## 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. Thanks!

abodein/netOmics