multiDEGGs: Multi-Omic Differentially Expressed Gene-Gene Pairs (original) (raw)
Performs multi-omic differential network analysis by revealing differential interactions between molecular entities (genes, proteins, transcription factors, or other biomolecules) across the omic datasets provided. For each omic dataset, a differential network is constructed where links represent statistically significant differential interactions between entities. These networks are then integrated into a comprehensive visualization using distinct colors to distinguish interactions from different omic layers. This unified display allows interactive exploration of cross-omic patterns, such as differential interactions present at both transcript and protein levels. For each link, users can access differential statistical significance metrics (p values or adjusted p values, calculated via robust or traditional linear regression with interaction term) and differential regression plots. The methods implemented in this package are described in Sciacca et al. (2023) <doi:10.1093/bioinformatics/btad192>.
| Version: | 1.0.0 |
|---|---|
| Depends: | R (≥ 4.4.0) |
| Imports: | DT, grDevices, graphics, knitr, MASS, magrittr, methods, parallel, pbapply, pbmcapply, rmarkdown, sfsmisc, shiny, shinydashboard, stats, utils, visNetwork |
| Suggests: | qvalue, testthat (≥ 3.0.0) |
| Published: | 2025-06-05 |
| DOI: | 10.32614/CRAN.package.multiDEGGs |
| Author: | Elisabetta Sciacca [aut, cre, cph], Myles Lewis [ctb] |
| Maintainer: | Elisabetta Sciacca <e.sciacca at qmul.ac.uk> |
| BugReports: | https://github.com/elisabettasciacca/multiDEGGs/issues |
| License: | GPL-3 |
| URL: | https://github.com/elisabettasciacca/multiDEGGs/ |
| NeedsCompilation: | no |
| Language: | en-gb |
| Citation: | multiDEGGs citation info |
| Materials: | README NEWS |
| CRAN checks: | multiDEGGs results |
Documentation:
Downloads:
Linking:
Please use the canonical formhttps://CRAN.R-project.org/package=multiDEGGsto link to this page.