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netOmics

This is the development version of netOmics; for the stable release version, see netOmics.

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


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("netOmics")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
netOmics HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GraphAndNetwork, Network, NetworkInference, Software, SystemsBiology, TimeCourse, WorkflowStep
Version 1.9.3
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.1)
Imports dplyr, ggplot2, igraph, magrittr, minet, purrr, tibble, tidyr, AnnotationDbi, GO.db, RandomWalkRestartMH, gprofiler2, methods, stats
System Requirements
URL https://github.com/abodein/netOmics
Bug Reports https://github.com/abodein/netOmics/issues
See More
Suggests mixOmics, timeOmics, tidyverse, BiocStyle, testthat, covr, rmarkdown, knitr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package netOmics_1.9.3.tar.gz
Windows Binary netOmics_1.9.3.zip
macOS Binary (x86_64) netOmics_1.9.3.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/netOmics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/netOmics
Bioc Package Browser https://code.bioconductor.org/browse/netOmics/
Package Short Url https://bioconductor.org/packages/netOmics/
Package Downloads Report Download Stats