netOmics

DOI: 10.18129/B9.bioc.netOmics    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see netOmics.

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

Bioconductor version: 3.15

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.

Author: Antoine Bodein [aut, cre]

Maintainer: Antoine Bodein <antoine.bodein.1 at ulaval.ca>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("netOmics")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("netOmics")

 

HTML	R Script	netOmics
PDF		Reference Manual
Text		NEWS

Details

biocViews	GraphAndNetwork, Network, NetworkInference, Software, SystemsBiology, TimeCourse, WorkflowStep
Version	1.2.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
License	GPL-3
Depends	R (>= 4.1)
Imports	dplyr, ggplot2, igraph, magrittr, minet, purrr, tibble, tidyr, AnnotationDbi, GO.db, RandomWalkRestartMH, gprofiler2, methods, stats
LinkingTo
Suggests	mixOmics, timeOmics, tidyverse, BiocStyle, testthat, covr, rmarkdown, knitr
SystemRequirements
Enhances
URL	https://github.com/abodein/netOmics
BugReports	https://github.com/abodein/netOmics/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	netOmics_1.2.0.tar.gz
Windows Binary	netOmics_1.2.0.zip
macOS Binary (x86_64)	netOmics_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/netOmics
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/netOmics
Package Short Url	https://bioconductor.org/packages/netOmics/
Package Downloads Report	Download Stats