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: 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

Need some help? Ask on the Bioconductor Support site!

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

Suggests	mixOmics, timeOmics, tidyverse, BiocStyle, testthat, covr, rmarkdown, knitr
Linking To
Enhances
Depends On Me
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Build Report	Build Report

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/
Package Downloads Report	Download Stats