netOmics

This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see netOmics.

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


Bioconductor version: Release (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")

BiocManager::install("netOmics")

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

Documentation

Reference Manual PDF

Details

biocViews GraphAndNetwork, Network, NetworkInference, Software, SystemsBiology, TimeCourse, WorkflowStep
Version 1.10.0
In Bioconductor since BioC 3.14 (R-4.1) (3 years)
License GPL-3
Depends R (>= 4.1)
Imports dplyr, ggplot2, igraph, magrittr, minet, purrr, tibble, tidyr, AnnotationDbi, GO.db, gprofiler2, methods, Matrix, 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
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Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
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
Package Short Url https://bioconductor.org/packages/netOmics/
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