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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: 1.0.0
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 ORCID iD [aut, cre, cph], Myles Lewis ORCID iD [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:

Reference manual: multiDEGGs.pdf
Vignettes: multiDEGGs vignette (source, R code)

Downloads:

Package source: multiDEGGs_1.0.0.tar.gz
Windows binaries: r-devel: multiDEGGs_1.0.0.zip, r-release: multiDEGGs_1.0.0.zip, r-oldrel: multiDEGGs_1.0.0.zip
macOS binaries: r-release (arm64): multiDEGGs_1.0.0.tgz, r-oldrel (arm64): multiDEGGs_1.0.0.tgz, r-release (x86_64): multiDEGGs_1.0.0.tgz, r-oldrel (x86_64): multiDEGGs_1.0.0.tgz

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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