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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 (>= 4.6.0) |
| 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 |
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) | |
| macOS Binary (big-sur-x86_64) | CorNetto_0.99.1.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/CorNetto |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CorNetto |
| Bioc Package Browser | https://code.bioconductor.org/browse/CorNetto/ |
| Package Short Url | https://bioconductor.org/packages/CorNetto/ |
| Package Downloads Report | Download Stats |