Multi-Omic Differentially Expressed Gene-Gene Pairs R package multiDEGGs version 1.2.1 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>. Software 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) Elisabetta Sciacca <e.sciacca@qmul.ac.uk> Comprehensive R Archive Network (CRAN) Elisabetta Sciacca [aut, cre, cph] (ORCID: <https://orcid.org/0000-0001-7525-1558>), Myles Lewis [ctb] (ORCID: <https://orcid.org/0000-0001-9365-5345>) GPL-3 2026-04-10 application/tgz https://CRAN.R-project.org/package=multiDEGGs doi:10.32614/CRAN.package.multiDEGGs en-gb