multiDEGGs: Multi-Omic Differentially Expressed Gene-Gene Pairs
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: | 1.1.3 |
| Depends: | R (≥ 4.4.0) |
| Imports: | DT, grDevices, graphics, knitr, MASS, magrittr, methods, parallel, pbapply, pbmcapply, rmarkdown, sfsmisc, shiny, shinydashboard, stats, utils, visNetwork |
| Suggests: | kernlab, nestedcv, pls, qvalue, randomForest, ranger, testthat (≥ 3.0.0) |
| Published: | 2026-02-02 |
| 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/, https://elisabettasciacca.github.io/multiDEGGs/ |
| NeedsCompilation: | no |
| Language: | en-gb |
| Citation: | multiDEGGs citation info |
| Materials: | README, NEWS |
| CRAN checks: | multiDEGGs results |
Documentation:
| Reference manual: | multiDEGGs.html , multiDEGGs.pdf |
| Vignettes: |
1. Differential Network Analysis (source, R code) 2. Feature Selection (source, R code) |
Downloads:
| Package source: | multiDEGGs_1.1.3.tar.gz |
| Windows binaries: | r-devel: multiDEGGs_1.1.2.zip, r-release: multiDEGGs_1.1.2.zip, r-oldrel: multiDEGGs_1.1.2.zip |
| macOS binaries: | r-release (arm64): multiDEGGs_1.1.3.tgz, r-oldrel (arm64): multiDEGGs_1.1.3.tgz, r-release (x86_64): multiDEGGs_1.1.3.tgz, r-oldrel (x86_64): multiDEGGs_1.1.3.tgz |
| Old sources: | multiDEGGs archive |
Linking:
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