CorNetto
This is the development version of CorNetto; to use it, please install the devel version of Bioconductor.
Knowledge-Guided Multi-Omic Correlation Network Analysis
Bioconductor version: Development (3.24)
Builds knowledge-guided multi-omic correlation networks from normalized transcriptomic, proteomic, and metabolomic abundance data. Group-specific correlation networks are compared with the Fisher z-difference test, either across all within-omic pairs in one or every assay without generating cross-omic pairs, or across candidate edges supplied by a prior-knowledge network, and the resulting differential network is summarized into node-level rewiring scores that identify features whose interaction patterns change between groups. Rewiring scores can be compared with group-label permutation reference distributions, and networks can be restricted to pathway-focused neighbourhoods, converted to 'igraph' objects, or exported as Cytoscape-ready node and edge tables. The package is built on Bioconductor containers so that multi-omic assays and sample metadata are managed consistently throughout the workflow.
Author: Bradley Ward [aut, cre] 
, Jean-Luc Balligand [ctb], Laurence Bamps [ctb], Patrice D. Cani [ctb], Julien De Greef [ctb], Joseph P. Dewulf [ctb], Vincent Haufroid [ctb], Benoît Kabamba [ctb], Sébastien Pyr dit Ruys [ctb], Didier Vertommen [ctb], Jean Cyr Yombi [ctb], Leïla Belkhir [ths, fnd], Laure Elens [ths, fnd], Sofina COVID Solidarity Fund [fnd]
Maintainer: Bradley Ward <bradleyalexward at gmail.com>
citation("CorNetto")):Bradley Ward. CorNetto: Knowledge-Guided Multi-Omic Correlation Network Analysis. doi:10.18129/B9.bioc.CorNetto, R package version 0.99.1, https://bioconductor.org/packages/CorNetto.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("CorNetto")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("CorNetto")| 1. CorNetto Workflow | HTML | R Script |
| 2. CorNetto COVID-19 Severity Workflow | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GraphAndNetwork, Metabolomics, Network, NetworkInference, Proteomics, Software, SystemsBiology, Transcriptomics |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0) |
| Imports | BiocParallel, graphics, igraph, methods, MultiAssayExperiment, S4Vectors, stats, SummarizedExperiment, tools, utils, withr |
| System Requirements | |
| URL | https://github.com/bradleyalexward/CorNetto |
| Bug Reports | https://github.com/bradleyalexward/CorNetto/issues |
See More
| Suggests | BiocManager, BiocStyle, knitr, qvalue, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CorNetto_0.99.1.tar.gz |
| Windows Binary (x86_64) | CorNetto_0.99.1.zip |
| macOS Binary (big-sur-x86_64) | CorNetto_0.99.1.tgz |
| macOS Binary (sonoma-arm64) | CorNetto_0.99.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CorNetto |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CorNetto |
| Package Short Url | https://bioconductor.org/packages/CorNetto/ |
| Package Downloads Report | Download Stats |