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
 [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/ |
| NeedsCompilation: |
no |
| Language: |
en-gb |
| Citation: |
multiDEGGs citation info |
| Materials: |
README NEWS |
| CRAN checks: |
multiDEGGs results |
Documentation:
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