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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
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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 |
Reference manual: | multiDEGGs.pdf |
Vignettes: |
multiDEGGs vignette (source, R code) |
Package source: | multiDEGGs_1.0.0.tar.gz |
Windows binaries: | r-devel: not available, 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 |
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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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