https://github.com/abodein/netomics
Multi-omics multi-layered network integration and interpretation
https://github.com/abodein/netomics
Last synced: 4 months ago
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Multi-omics multi-layered network integration and interpretation
- Host: GitHub
- URL: https://github.com/abodein/netomics
- Owner: abodein
- License: gpl-3.0
- Created: 2021-04-13T19:06:30.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2024-10-15T13:23:10.000Z (over 1 year ago)
- Last Synced: 2025-09-08T11:20:53.581Z (10 months ago)
- Language: R
- Size: 31.8 MB
- Stars: 14
- Watchers: 1
- Forks: 4
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Awesome Lists containing this project
README
[]
(https://travis-ci.com/abodein/netOmics)
[]
(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 ()
## Bugs/Feature requests
If you have any bugs or feature requests,
[let us know](https://github.com/abodein/netOmics/issues).
Thanks!