netOmics
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see netOmics.
Multi-Omics (time-course) network-based integration and interpretation
Bioconductor version: 3.14
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("netOmics")):
Installation
To install this package, start R (version "4.1") 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")| netOmics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GraphAndNetwork, Network, NetworkInference, Software, SystemsBiology, TimeCourse, WorkflowStep |
| Version | 1.0.0 |
| 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_1.0.0.tar.gz |
| Windows Binary | netOmics_1.0.0.zip |
| macOS 10.13 (High Sierra) | netOmics_1.0.0.tgz |
| 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 |
| Old Source Packages for BioC 3.14 | Source Archive |