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: | 1.1.1 |
| 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: | 2025-10-24 |
| 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 |
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